I too am having the same issue. I am running a fairly clean copy of Retropie v3.4 on a Raspberry Pi 2. So far the only changes I have made are to add a couple of bluetooth devices and a Udev rule for one of them.
I am attempting to load the roms from a 16Gb SanDisk USB formatted to Fat32 with less than 2Gb of data on it using Retropie’s built in copy service.
All the roms copied across for systems named A-S(Scummvm), up until it got the the Snes folder where I had a 0% success rate. The same applied to the ZXSpectrum. The files look fine to me, the folder structure has not been changed from when the copy service created them. At the moment I am at a loss as to why they don’t copy across, but I will continue to investigate when I get the chance.