I've tried FAT32 and ex-FAT. The DX90 recognises it, but refuses to do a scan of it. It will start, and the orange bar will never appear. I can manually scan the files in, but it does the same thing after every 20 or so files. It seems to be freezing less frequently now, but I'm only down to artists beginning with the letter C...
Another oddity I've encountered is with 'ée'. My DX90 seems to create three of the same artist, but the 'ée' in the last two is replaced with Japanese/Chinese characters. Here's a picture:
Somewhat unsurprisingly, these glitched artists and albums cause the DX90 to freeze.
You might want to skim the DX50 FAQ, there's a few pointers on making sure the files on the card are squeaky clean or scanning will freeze. Have you tried adding one artist folder at a time to see if it's a specific file that crashes it? It'll help a lot when trying to troubleshoot the issues.