After properly formatting to fat32 with the GUI utility my SanDisk Ultra 64gb (part#SDSDQUA-064G-A11A) has had no issues with the X3 in terms of the flac and mp3 files folders (music-4 subfolders-artist-album-song) being indexed, read, played, album art displayed. The x3 also seems to read the card quickly (have it set to auto).
I don't know if there are inconsistencies with the SD cards but I got this one new from Newegg and it has performed well and gotten along with the X3. After reading about the problems others were having I did make sure I had everything properly tagged using Foobar and mp3tag.
What is the size of his music archive, and also how many folders and tracks are there in total?