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When the debugger hits a breakpoint and NB's window is not the current active window, then NB 3.x activated its window (resulting in a short blinking in the task bar (Windows 2000)). NB 4.0 does not do that anymore. So, you don't know, when the breakpoint is being hit, if you are using another program (for example web browser) at that time.
*** This issue has been marked as a duplicate of 19292 ***
Verified ... and Closing all issues resolved into NetBeans 6.7 and earlier.