I tried downloading Metal Slug from REMOVED do not post romsites! and switching it for the working version of M. Slug that I have on my RetroPie. It didn’t work. So I’m convinced that you’ve got one of those infamous ROM incompatibility issues.
I’m lucky enough to own a ROM set that I downloaded years ago. That GeoGeo and Mame set works w/ the versions of the emulators in RetroPie.
I guess that you should ask help on converting your ROM set to and older version and check that the BIOS file you have works too. I don’t know if the BIOS Zip file needs to be of a certain version too. In the links that the others gave you above there appears to be a method of converting ROMs if I’m not mistaken.