This is a post mortem in case someone with the same issue comes here looking for help, I fixed the issue.
I noticed yesterday that some of my customs were unplayable (list below). When you scroll to the song in the library the sample does not play and the album cover is replaced by a white square. When you select the song you can choose difficulty and stuff, but when you start the song it says something along the lines of, "Unable to load song, skipping track" and spits you back out to the library. I tried a couple of things I saw posted about here in threads about people getting the same error, but my problem appears to be different since those solutions didn't work for me. One thing I did not do was delete the song cache, which I was hoping not to have to resort to for obvious reasons.
The thing that worked was scrolling through the in game library and finding all of the tracks that were broken (easy since the album covers were all white squares), deleting each one through the in game library (this took a while because the damn thing remakes the song cache every time you delete a song), re-downloading them from the C3 database, making them into a song pack in the con tools, and then adding that to my USB drive.
Many of the bugged songs were recent downloads (marked with a *) for me, but some of them were quite old. Not sure if there is any rhyme or reason to it, or just a random glitch.
1,000,000 - Nine Inch Nails