That is odd, I prefer folders too but it should not make it faster, likely slightly slower. Slow is relative, how many seconds does it take now to load? I think you should try different USB flash drives as they all varies in performance, and make sure they are formatted FAT32, not exFAT or NTFS. I am guessing most AVRs don't like exFAT an NTFS even though they are much better than FAT32.