Using the Jalopy plug-in can potentially lead to problems if you are also using Jalopy as a command-line tool, Netbeans, Ant or other plug-in because the file formats in Jalopy's home directory .jalopy where it stores all its settings have changed.

The latest Jalopy version available from http://jalopy.sourceforge.net/ is 1.0b10. Please note, that the Jalopy plug-in listed on jEdit's plug-ins page is an older version (1.0b7) which is not compatible with the config files of 1.0b10.

I had already been using Jalopy's Ant plug-in. Installing the jEdit Jalopy plug-in led to my settings being replaced by Jalopy's default settings; the config files written by jEdit's Jalopy plug-in were unrecognized by my Ant plug-in and builds (from the command line) failed.

On http://jalopy.sourceforge.net/ there is a newer jEdit plug-in (1.0b10), which is compatible with the other plug-ins also available on this site.

Removing the plug-in I had downloaded on the jEdit site and replacing it with the one from the Jalopy site resolved the conflict.