Reported with NetBeans:

Product Version: NetBeans IDE Dev (Build 201206110001)
Java: 1.7.0_05; Java HotSpot(TM) 64-Bit Server VM 23.1-b03
System: Mac OS X version 10.7.4 running on x86_64; US-ASCII; en_US (nb)

Primary screen is the macbook, secondary is LCD, positioned above.

IDE is on external monitor, invoking popup shows it either too high running out of screen or accross both screens.

See screenshots at
http://bugzilla-attachments-214032.netbeans.org/bugzilla/attachment.cgi?id=120720
http://bugzilla-attachments-213984.netbeans.org/bugzilla/attachment.cgi?id=120676

The original NetBeans bugs:
http://netbeans.org/bugzilla/show_bug.cgi?id=214032
http://netbeans.org/bugzilla/show_bug.cgi?id=213984