@johnes
Broadly speaking if you have a Pi3 the mame-2003 emulator is a good bet with the 0.78 romsets.
If you want to stick with the 0.375b then I'd use lr-imame4all - not least because it will allow all the Retroarch functionality as well as easier controller file config.

If you just want to enable a shader (including the one mentioned in the thread you list above), I would strongly recommend using the inbuilt configuration editor:
https://github.com/retropie/retropie-setup/wiki/Configuration-Editor

@Chillimonster you need to make a transparent .png file then add it in the overlays folder. Thne name it something like none.png

I'd recommend using the configuration editor to manage your configs:
https://github.com/retropie/retropie-setup/wiki/Configuration-Editor

You may want to check your system specific retroarch file isnt holding a mass of non-required configs now, there is usually just 4 or 5 lines in there.
A bit like this:
http://pastebin.com/n5FbDBUK

What about crt-hylllian-glow and crt -easymode?
Thanks

I dont have a solution, sorry, for me its been the same since june.

I think you will be better off asking here:
https://forum.recalbox.com/

I've not really looked at the structure of Recalbox before.