Sorry for the late response. I don't visit as often as I used to.
It's important to realize that it doesn't matter whats displayed on the artwork. (3D, spine, flat, don't matter) What IS important is how the artwork is saved. All PNG files need to have a 32bit color depth. They also need to have a specific resolution. I was able to get an image resolution of 180x248 to work pretty successfully. I was also able to get a double resolution of 360x496 to work. And though these covers look cleaner, at this increased resolution, they also load slower because of the increased file size.
Which ultimately may end up limiting how many roms you can have per folder when using covers saved at higher resolutions. Genplus "can" handle long game lists, but if I recall correctly the Wiis memory isn't able to cache all the larger artwork files simultaneously.
So, when using a bunch of higher res images, you either get slower scrolling, missing images, or even no images at all.
I'd say make sure my suggestions above have all been considered. Then try testing with a limited amount of files at first. Also, another quick test is to take one of your working Genesis covers and simply name it after one of your master system games. Then place that renamed cover in the Master System folder. If the cover displays when you select your specific MS game, then you know it's an issue with your MS cover set. If it doesn't work, and it should, then I'm out of ideas, because that's not how this emulator works.
It's simply looking for artwork (any artwork) that meets certain file criteria, and associates it with whichever rom shares the same name.
Hope I was able to help.