I was running into this exact same problem, and was about to throw my pi through a window. Here’s how I fixed it.
I used the SD card image found at the beginning of the post on this blog that shows you how to do it under ‘Major Time Saving Update’. I tried the long way at first and it took 16 hours. NOT DOING THAT AGAIN.
After that, I unzip my ROMS first, then move the extracted ROM to the corresponding folder -> NES, SNES, etc
Then I went to NO-LINKS-ROMS-SITES-PLEASE – best place ever. I donated, and now, I don’t have a problem with ROMS at all. EVER.
For some reason though, the PI places 2 titles for each ROM in the list, not sure how to fix that just yet, and the volume seems to be a little low for the games, but other than that. Works perfectly.
This is an awesome site, and thanks to whomever runs it for the guide. Saved me from throwing my entire computer desk into a lake.
Hope that helps!