I refreshed the page and jumped around the webui a little and it was still at sync filesystems. About a half hour ago I hit the shutdown button which didn't do anything, so I used the poweroff command from the web terminal which made the webui go blank but didn't actually power down the server. I had to hold down the power button and once I booted up again it still said that the shutdown was unclean. Thanks for looking btw, this is driving me nuts.
Some other things I've tried just to see is run a hw test on my flash drive, check all my discs for errors and make sure I'm at stock cpu and mem timings.