I recently compiled Nestopia for my Ubuntu HTPC with the idea of running it from XBMC using the launcher. The launcher works fine but I am having trouble getting the emulator working in fullscreen mode. At the moment when using the Scale HQx setting with 4x scaling and fullscreen toggled, the vertical alignment is correct, but the the horizontal alignment is off by about a quarter of my display (i.e. the fullscreen mode is shifted off the screen by a quarter). I have a clean install of ubuntu on a core i3 sandybridge powered computer using the intel hd 2000 onboard graphics. I haven't done anything with proprietary drivers.
Any information on how to fix this would be great. I searched on google but the documentation for nestopia on linux seems very minimal.
Let me know if you need any more information.