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 sort of hangs after each song. When I leave it long enough, the next song plays, but the unit is "hung" and it can take several minutes before the song name changes and the UI is responsive. In playing with it I found that by hitting the menu button, the unit frees up and shows the next song until it needs to change songs again.
I can only say this is a real dissappointment considering I'd like to have that 32 gig thumbdrive or SD card with 10k songs on it. Thes units are not cheap, and handling 10k files should not be a problem. An IPOD does it fine! And before any one says it, I don't need or want an IPOD. This unit should work fine with plain media and MP3s.
Does anyone have a similar story and are there any ideas on what causes it? File sizes? File names too long? Bad filke names? Number of songs too large? Media class (I got an 8 gig class 6 SD card and these problems occur)? Random play lookup?