try apple.laf.useScreenMenuBar=false to make menus stay closer to the editor views they belong to -- potentially less confusing for jEdit newcomers;
--- a/src/Tools/jEdit/etc/settings Wed Mar 21 11:36:47 2012 +0100
+++ b/src/Tools/jEdit/etc/settings Wed Mar 21 13:54:33 2012 +0100
@@ -6,7 +6,7 @@
JEDIT_OPTIONS="-reuseview -noserver -nobackground -log=9"
JEDIT_JAVA_OPTIONS="-Xms128m -Xmx1024m -Xss4m -Dactors.corePoolSize=4 -Dactors.enableForkJoin=false"
#JEDIT_JAVA_OPTIONS="-Xms128m -Xmx512m -Xss2m -Dactors.corePoolSize=4 -Dactors.enableForkJoin=false"
-JEDIT_SYSTEM_OPTIONS="-Dapple.laf.useScreenMenuBar=true -Dcom.apple.mrj.application.apple.menu.about.name=Isabelle/jEdit"
+JEDIT_SYSTEM_OPTIONS="-Dapple.laf.useScreenMenuBar=false -Dcom.apple.mrj.application.apple.menu.about.name=Isabelle/jEdit"
JEDIT_STYLE_SHEETS="$ISABELLE_HOME/etc/isabelle.css:$JEDIT_HOME/etc/isabelle-jedit.css:$ISABELLE_HOME_USER/etc/isabelle.css:$ISABELLE_HOME_USER/etc/isabelle-jedit.css"