freezway: This is caused from you using an old, old version which exhibited this bug, caused by the updater not asking for a program restart after updating the jar. The fix would be to download and use a newer version, but workarounds exist.
You must first shut down the program. At this point, you almost definitely have an outdated enigma dll/so which may or may not work, so it needs rebuilding. LGM+plugin does not know to rebuild it automatically (in your version). 3 ways to force a rebuild:
1) The recommended way: Delete libCompileEGMF.so or compileEGMf.dll.
2) Wait for another update to come around, which should cause enigma to update and rebuild when you run LGM+plugin.
3) Build it yourself, using any approved builder (such as Make or C::B).
Once you have done this, simply run the program (unless you chose option 2, in which case the program is already running). If you chose option 1, LGM will issue a rebuild. Otherwise, LGM should pickup the newly built enigma and work with it.
A possible 4th way does exist, if you have upgraded LGM+plugin to a new enough version. This was the way that we solved the problem.
4) (java) Preferences.userRoot().node("/org/enigma").putBoolean("NEEDS_REBUILD",true);
(basically, in windows, this adds an entry to the registry somewhere called NEEDS_REBUILD with value of true. In linux, it does so with a file somewhere.) The next time LGM+plugin is run, it will read this entry, realize that it needs rebuilding, and do so.