You certainly aren't the only one having these types of issues. I think you aren't getting responses because it's in the wrong sub-forum. The guys that work on crt emu are in the Groovymame forum.
It is very obvious that crt emu is designed to work well with Groovymame as everything comes out perfect. I'm having similar issues (and others) when I try and use other emulators. I thought it was the super resolutions that were causing the issues as that is all was generated in mine. I have no native resolutions at all in my list.
I can see why super resolutions work for sprite based games where graphics are pre-drawn but I suspect that, in 3d games with real-time rendering, generation a super wide resolutions puts a strain on my gpu. I can't make Model 2 or model 3 games work well in 2560 x 384 but they work fine in 640 x 480. I need to figure out how to add 496 x 384 instead for my ega games.