So first off, the original firmware has no issues. Strangely, neither does rockbox...
Several days ago in a vain attempt to make the thing work, I wiped the card all except for a few hundred megs of music and it worked fine. Realizing later in the day I was no longer able to troubleshoot my problems, I added 10 gigs of music to try to recreate the problem. Everything ran fine on the original firmware, and other than some database cataloging issue ran fine on rockbox. I then reloaded the same files I originally had onto the card yesterday and so far it had been running fine.
I have also noticed some peculiarity in the database where it saved multiple entries of one song. when it compiles a database, there can be at least five links to the same file. I think this could have something to do with the problem, especially because I have not created a database for its current files yet.