System: 

Windows XP 32bit, Dual-core AMD64, Java 1.5.0_06, Netbeans 55qbuild1 and 5.0final. 

After (multiple) clean installs, after opening one or more projects, Netbeans
threw an exception during "Scanning project classpaths". In
var/log/messages.log, we saw lots of exceptions like this: 
java.io.FileNotFoundException: C:\Documents and
Settings\username\.netbeans\5.0\var\cache\mdrstorage\org-netbeans-java\0.70\f1f41dec8793b72596335c2b6b4bdaefe45bf5f86htsserverlibclient.btx
(The process cannot access the file because it is being used by another process)
	at java.io.RandomAccessFile.open(Native Method)
	at java.io.RandomAccessFile.<init>(RandomAccessFile.java:98)
	at
org.netbeans.mdr.persistence.btreeimpl.btreestorage.FileCache.getFile(FileCache.java:109)

Will attach a complete messages.log. 

This led to all sorts of problems in the IDE, mostly related to the metadata
facility (code completion, goto source/definition, even "Run File").
Furthermore, there seems to be bugs in the error handling: Sometimes we got a
dialog box showing a NPE, and on closing this dialog box a new one popped up.
Terminating all netbeans processes using TaskManager was the only way to exit
netbeans at this point. The NPE dialog box appeared by itself sometimes, but
mostly as the error icon in lower right statusbar, and when clicking on that
icon the IDE entered the NPE loop. 

This is a complete showstopper, and only several hours of debugging and
experimenting made us able to run Netbeans again. We believed the problem to be
related to the dual-core / multiprocessor architecture and tried the following
workarounds:
 - using imagecfg.exe -u on netbeans.exe (restricting all netbeans processes to
a single CPU) 
 - AND un-setting netbeans_default_options in netbeans.conf (i.e. stopped using
-J-XX:+UseConcMarkSweepGC)

This workaround seems to have eliminated the problem.