Out of curiository, I tried the Final Burn version provided by the RetroPie distribution (well, the script, from Raspbian).
Strangely, it uses a kind of meta-config file common to all emulators and somehow applies to Final Burn Alpha !
I noticed a few strange things. In this version of your emulator, a 640x480 resolution is used (well, that's what my monitor says) while my monitor remains in 1280x1024 when I start the stock Final Burn build. It seems to make a little difference in rendering. I'm not 100% sure but for some reason I find it less blurry in 640x480. Strange ! Is it possible to force another screen resolution in the regular fba2x.cfg ?
Also I noticed something else. Earlier I mentioned that the display ratio in Final Burn was not correct in all games. For instance, 3Wonders or Striders look "squashed". It's OK by default in the RetroPie build. Then I realized I could get the right ratio in the regular FBA burn as well by... disabling the correct aspect ratio in the config file. (?)
Strange ?
Well there are some more differences in the 2 builds but that's not the point of this thread anyway
Well... Thanks again for you work which makes the Pi extremely enjoyable ! Definitely looking forward to some more improvements. Tell us if we can help somehow !