NetBeans IDE Dev (Build 200703181900)
1.6.0; Java HotSpot(TM) Client VM 1.6.0-b105
Linux version 2.6.16-1.2122_FC5 running on i386
en_US (nb); UTF-8

Example (ThreadSuspending.java test in debugger testspec):

for (int i = 0; i < 100; i++) {
    i++;
>    System.out.println("Thread-2: " + (i));
    i--;
}

> is line breakpoint

1. start debugging
2. stop on the breakpoint
3. invoke step over four times

A question dialog will appear with "Step was interrupted by breakpoint ..." message.
Answer Yes (the breakpoint should be ignored).
Result:
Current pc annotation disappear, debugger is running by content of toolbar,
threads view, sessions view and debugger console. 
Local variables, watches and output of the application looks like the debugger
is stopped - no new message from System.out, the same values of variables.