in 7.0.1 patch 2 it works nicely.
gdb log for 7.0.1:

~"GNU gdb 6.8.0.20080328-cvs (cygwin-special)\n"
~"Copyright (C) 2008 Free Software Foundation, Inc.\n"
~"License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\n"
~"This is free software: you are free to change and redistribute it.\n"
~"There is NO WARRANTY, to the extent permitted by law.  Type \"show copying\"\n"
~"and \"show warranty\" for details.\n"
~"This GDB was configured as \"i686-pc-cygwin\".\n"
&"C:\\\\Users\\\\ap153252/.gdbinit: No such file or directory.\n"
(gdb) 
2-list-features
3-gdb-set print repeat 0
4-gdb-set backtrace limit 1024
5-gdb-set print elements 0
6-file-symbol-file "C:/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/dist/Debug/Cygwin_4.x-Windows/welcome_xxx"
7-file-exec-and-symbols  "C:\\Users\\ap153252\\Documents\\NetBeansProjects\\Welcome_xxx\\dist\\Debug\\Cygwin_4.x-Windows\\welcome_xxx"
2^done,features=["frozen-varobjs","pending-breakpoints"]
(gdb) 
3^done
(gdb) 
4^done
(gdb) 
5^done
(gdb) 
6^done
(gdb) 
7^done
(gdb) 
8-file-list-exec-source-file
9cd C:\Users\ap153252\Documents\NetBeansProjects\Welcome_xxx
10-exec-arguments "arg 1" "arg 2" "arg 3" "arg 4"
11set environment Path=C:\cygwin\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Java\jdk1.6.0_21\bin\;C:\Program Files (x86)\QuickTime\QTSystem\;C:\cygwin\bin;C:\Program Files (x86)\Calibre2\
8^done,line="24",file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",macro-info="0"
(gdb) 
12-break-insert -f "C:/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc:38"
1
13-break-insert -f "C:/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc:45"
1
14-break-insert -t main
15-exec-run
16info threads
&"cd C:\\Users\\ap153252\\Documents\\NetBeansProjects\\Welcome_xxx\n"
~"Working directory /cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx.\n"
9^done
(gdb) 
10^done
(gdb) 
&"set environment Path=C:\\cygwin\\bin;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files\\Java\\jdk1.6.0_21\\bin\\;C:\\Program Files (x86)\\QuickTime\\QTSystem\\;C:\\cygwin\\bin;C:\\Program Files (x86)\\Calibre2\\\n"
11^done
(gdb) 
12^done,bkpt={number="1",type="breakpoint",disp="keep",enabled="y",addr="0x00401254",func="main",file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="38",times="0"}
(gdb) 
&"\n"
1^done
(gdb) 
13^done,bkpt={number="2",type="breakpoint",disp="keep",enabled="y",addr="0x004012f8",func="main",file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="45",times="0"}
(gdb) 
&"\n"
1^done
(gdb) 
14^done,bkpt={number="3",type="breakpoint",disp="del",enabled="y",addr="0x0040122b",func="main",file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="33",times="0"}
(gdb) 
15^running
(gdb) 
~"[New thread 4768.0xf54]\n"
&"Error: dll starting at 0x76aa0000 not found.\n"
&"Error: dll starting at 0x74a60000 not found.\n"
&"Error: dll starting at 0x76aa0000 not found.\n"
&"Error: dll starting at 0x76bc0000 not found.\n"
No command for record 1^done
No command for record 1^done
~"[New thread 4768.0x10c8]\n"
15*stopped,thread-id="1",frame={addr="0x0040122b",func="main",args=[{name="argc",value="5"},{name="argv",value="0xb59560"}],file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="33"}
(gdb) 
&"info threads\n"
~"  2 thread 4768.0x10c8  0x76ebf8f5 in ntdll!RtlUpdateClonedSRWLock ()\n"
~"   from /cygdrive/c/Windows/system32/ntdll.dll\n"
17-stack-list-frames
~"* 1 thread 4768.0xf54  main (argc=5, argv=0xb59560) at welcome.cc:33\n"
16^done
(gdb) 
17^done,stack=[frame={level="0",addr="0x0040122b",func="main",file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="33"}]
(gdb) 
18-stack-list-arguments 1
18^done,stack-args=[frame={level="0",args=[{name="argc",value="5"},{name="argv",value="0xb59560"}]}]
(gdb) 
19-exec-next
19^running
(gdb) 
19*stopped,reason="end-stepping-range",thread-id="1",frame={addr="0x00401230",func="main",args=[{name="argc",value="5"},{name="argv",value="0xb59560"}],file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="35"}
(gdb) 
20-stack-list-frames
20^done,stack=[frame={level="0",addr="0x00401230",func="main",file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="35"}]
(gdb) 
21-stack-list-arguments 1
21^done,stack-args=[frame={level="0",args=[{name="argc",value="5"},{name="argv",value="0xb59560"}]}]
(gdb) 
22-exec-next
22^running
(gdb) 
22*stopped,reason="end-stepping-range",reason="breakpoint-hit",bkptno="1",thread-id="1",frame={addr="0x00401254",func="_fu0___ZSt4cout",args=[],file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="38"}
(gdb) 
23-stack-list-frames
23^done,stack=[frame={level="0",addr="0x00401254",func="_fu0___ZSt4cout",file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="38"}]
(gdb) 
24-stack-list-arguments 1
24^done,stack-args=[frame={level="0",args=[{name="argc",value="5"},{name="argv",value="0xb59560"}]}]
(gdb) 
25-exec-next
25^running
(gdb) 
25*stopped,reason="end-stepping-range",thread-id="1",frame={addr="0x00401260",func="_fu0___ZSt4cout",args=[],file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="39"}
(gdb) 
26-stack-list-frames
26^done,stack=[frame={level="0",addr="0x00401260",func="_fu0___ZSt4cout",file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="39"}]
(gdb) 
27-stack-list-arguments 1
27^done,stack-args=[frame={level="0",args=[{name="argc",value="5"},{name="argv",value="0xb59560"}]}]
(gdb) 
28-exec-next
28^running
(gdb) 
28*stopped,reason="end-stepping-range",thread-id="1",frame={addr="0x00401294",func="_fu1___ZSt4cout",args=[],file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="40"}
(gdb) 
29-stack-list-frames
29^done,stack=[frame={level="0",addr="0x00401294",func="_fu1___ZSt4cout",file="welcome.cc",fullname="/cygdrive/c/Users/ap153252/Documents/NetBeansProjects/Welcome_xxx/welcome.cc",line="40"}]
(gdb) 
30-stack-list-arguments 1
30^done,stack-args=[frame={level="0",args=[{name="argc",value="5"},{name="argv",value="0xb59560"}]}]
(gdb)

looks like a race condition in current line annotation setting

cnd sets correct line for the current PC annotation but for some reason annotation sticks to the nearest following annotation in the editor (in our case - breakpoint). Interesting observations:
1. if user remove breakpoint annotation or reopen the file - it all reappears correctly (i.e. all annotations appears where they should)
2. it all happen only if before the step current PC annotation was on the same line as another breakpoint annotation (visible mixed annotation)
It all worked in 7.0.1, could it be a change in editor that causes this behavior?

it looks like this performance optimization is the cause (Annotations.java:401):
...
else if (lastGetLineAnnotationsLine + 1 == line && lastGetLineAnnotationsIdx + 1 < lineAnnotationsArray.size()) {
                    annos = (LineAnnotations)lineAnnotationsArray.get(lastGetLineAnnotationsIdx + 1);
                    lastGetLineAnnotationsIdx++;
                    lastGetLineAnnotationsLine = annos.getLine();
                    lastGetLineAnnotationsResult = annos;
                    return annos;
                }

if I comment these lines everything works perfect

Created attachment 113717 [details]
proposed patch

Thanks for the patch. I did the change for getLineAnnotations (only tried to make the diff smaller). For getNextLineWithAnnotation, the current behavior is actually correct: the method should return the line number of a next line with annotations. Which, as I read the code, is exactly what happens.

http://hg.netbeans.org/jet-main/rev/337b947a2692

Marian, Jirka, please let me know if this should go to 7.1.

(In reply to comment #7)
> Marian, Jirka, please let me know if this should go to 7.1.

Alexander, or anybody from CND : is it stopper for you (and the only reason to rebuild FCS) ? 

My personal preference is to fix it into patch (means 7.1.1).

cnd QA thinks it is a showstopper (and a regression) and must be fixed in 7.1

The patch seems ok to me.

Ok, integrate into release71, ASAP please.

release71:
http://hg.netbeans.org/releases/rev/a03ccf7e25a4

Please verify.

Integrated into 'releases'
Changeset: http://hg.netbeans.org/releases/rev/a03ccf7e25a4
User: Jan Lahoda <jlahoda@netbeans.org>
Log: #205774: make sure that the last cache is used in getLineAnnotations only if the next annotation's line actually matches the provided line.

Integrated into 'main-golden'
Changeset: http://hg.netbeans.org/main-golden/rev/337b947a2692
User: Jan Lahoda <jlahoda@netbeans.org>
Log: #205774: make sure that the last cache is used in getLineAnnotations only if the next annotation's line actually matches the provided line.

Verified in FCS build 20111203