How many main folders do you have and what position is your mame folder. I had similar problems. I uploaded 4 mame games. Then synced just them and the 30 and it worked. Then when I add them in with all my games and made a mame folder for them 1 of the 4 games wouldn't work. Tried making another main mame folder with 2 games in one and 2 in the other. Synced again and same thing still the 1 out of 4 wouldn't work. Then combined them in same folder again and made the mame folder sync 2nd instead of 6th and it fixed my problem. I also deleted a gameboy advance game but I don't think I needed to. So try moving your mame folder to sync like first.
Last night when I was syncing, the folder structure remained the same as it always has. When I synced last night all the folders were there, there just wasn't any games in them. I just synced the two neo geo games and I had them in the S-Z folder. Now after adding all my other games like you did, I'm getting this error. I deleted some games and am now syncing again. If I can remember correctly, I think my 'mame' folder (Which I have it named Arcade in the folder menu) syncs right after the original 30 if that makes sense.