I can't no longer run roms off the usb storage either since doing a clean install of retropie 4.2. Nothing works. Even using this guys hack [link text]
(link url) and following these instructions [link text]
(link url) no longer work.
Emulation station was updated which broke a lot of things even my controllers were messed up I was able to fix them but the last two days made me want to trash my PI and just stay with playing games on my PC.
The only workaround was I had to get a bigger SD card and run the roms off of there, nothing else worked.