I've traced this farther down into URLDeploymentScanner. When I enable trace for the URLDeploymentScanner, it never shows it trying to deploy my exploded JAR (which is the problem).
I can't see any reason why this should fail. Yes, my directory has a dot in it, but it should still be added as a URL to check.
Cause was found and seemingly unrelated. My HSQLDB data files were corrupted somehow. I had almost 1GB of data in them.
When I was debugging with jdb, I noticed that the HSQLDB service was trying to be deployed before my exploded JAR. The deploying of the HSQLDB service was never finishing because of a huge delay, thus my files were never getting deployed since they were to be deployed after HSQLDB.
Hope this helps someone else! I did this via a low-level jdb debug since it was on a remote Linux machine, would've been nicer within Eclipse.