@Monica About one year later after your question, I've experienced the same issue with Mountain Lion (according to jEdit's homepage, 5.1.0 is still the current stable version).
I've installed jEdit in /Applications/Dev/
(not /Applications
as most people do, I believe; that's not important except for designating the path, see below). I'm using Java 7.
The following works for me from the command line, like for you:
java -jar /Applications/Dev/jEdit.app/Contents/Resources/Java/jedit.jar
So, I used Automator to create a normal MacOS Application named "MyJEdit.app" as in the screenshot. Now I can launch MyJEdit instead of jEdit. Other java flags might be required, for instance to set the memory usage (cf java -help
and java -X
).