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Since I upgraded to NB 3.3.1 I can't add a breakpoint (either clicking on button or on line number or with Shift-F8). See ide.log for stack trace.
Created attachment 4705 [details] ide.log
I could not reproduce this bug. So I found a probable cause of the trouble (thanks to the log you have provided) and fixed it (I hope). Please try a development version of NetBeans and re-open this issue if you still encounter the problem. Monday night build (200202250100?) should contain the fix. Development builds are available from http://www.netbeans.org/downloads-dev.html.