I have loads of these external usb drives (around a dozen lol) and some of them do really wierd things.
The most annoying is that they can do a kind of soft reset during load (not all of them) and so you can read from the drive for a few seconds.
Maybe you could try to split your music up in to subfolders under the music folder (rock, pop, rap, dance, punk, emo etc, or a-f, g-l, m-s, t-z)
Then add one folder at a time to the music folders in Subsonic.
Also, I would do a checkdisk on the USb drive to check for any possible errors.
Failing that, copy some of the files subsonic has reported as failing on to your local hard disk, and try getting subsonic to recognise them.
Should keep you busy
Good luck with the 3.9 rollback, I am considering that myself due to the issues I am having
Alan.