I guess you could create a ticket, it never hurts to capture any findings. It is unlikely, that I am going to fix it, though. Somebody has to take over the ownership of the code base, I don't have much time to deal with it anymore. I might fix something JIT related, but any other change is out of the scope of the original project, I was just too enthusiastic with the improvements (what I regretted later).
problems with gfx_vsync=true
Sounds like this is an issue with the SDL library I linked to the project. I am not an expert on SDL and I had no intention to support the SDL build. Maybe somebody else can create a new build which works better. Is this the version you tried? http://os4depot.net/index.php?function=showfile&file=emulation/computer/e-uae-sdl.lha
Have you tried without JIT with version 1.0.0? Also, could you please specify the screen type/resolution you are using?
Mike's improvements
Patch to fix the overlay mode on MorphOS
Patch to make E-UAE compile with latest SDK includes
Thanks for the patch. I am going to include the changes in the next release.