I've been having the same problem with MP3 files not playing from SD card. I used to have no problem playing music from the SD card. There is nothing else on the card, and it's formatted FAT32. Haven't found a fix yet.
It's like the software is not scanning for new music on the SD card. I don't have an IPod so it shouldn't have anything to do with the VR Catalog Mode setting. I have it set to "on" just in case.