I got an F90BT in June and returned it after your problem and another with USB songs being cutoff toward the end on v2.0 made the unit unusable for me. I replaced it with an X910BT and v3 SW which fixed the MP3 songs being cutoff, but not the slow boot up and other problems with a lot of songs. The Pioneer manual quotes that both the SD card and USB are limited to 8 gig in the X910BT.
But I also find that both a thumbdrive and a SD card with more than around 600 songs is a real problem. The deck will load them slowly like you noted, then begin playing them, but after a song or two it