I've found something interesting : when i open Global Option and i go to "Appearance", jEdit put a line in my "properties" file "lookAndFeel=com.apple.laf.AquaLookAndFeel" even if i do anything. After a restart the CMD-V in search and replace dialog stop working.
If i remove this line from the properties file I can CMD V again in search and replace dialog, and the appearance of jEdit don't change at all
I use the "Mac OS X Support plugins" (1.1)
In "Options > jEdit > Appearance > Swing look & feel" "Mac OS X" is selected
Mac OS X 10.6.2, - jEdit 4.3.1 - Java 1.6.0_17
This issue has already been fixed and is a duplicate of tracker item #2956477
It was a plugin patch, and has been fixed:
https://sourceforge.net/tracker/?func=detail&atid=997937&aid=2959723&group_id=588
will be included in next version