Well to update on my media scanning problems, I had tried everything, trading my memory card to other devices where it worked fine, using the firmware upload tool that ibasso provided...etc., etc. with no resolution of my scanning problems.
Contrary to logic, even though the microsd card worked fine in every other device, I eventually tried a card from another device in the DX90. It works! I don't know why.
Anyway, scanning of 6000 plus files takes approximately 20 minutes, but afterwards all files show and do not come up as "null". I can now shuffle amongst all files on the device without manual file by file scanning...Yeah!
My remaining main problems are the ongoing cutouts during songs (which I do not notice when using the line out), and the media scanning is still a little wonky. I added a few songs to the device. Upon disconnecting from the computer it did a quick scan but did not find the new tracks. I then manually searched for a new track via directory view and when I tried to play it, it automatically started an entirely new scan again. When finished the tracks were recognized.
Major remaining problems:
1. Song cutouts mostly noticed on HO and Coaxial Out.
2. Slow GUI response, particularly on "All Music" tab.
3. Freezing up if actions are done too quickly or at the same time. This issue occurs consistently if I'm searching a file list for a song while it is playing, and I attempt to change the volume at the same time.
3. Finicky media scanning that is still a little unpredictable.