10.8.1 won't let me upgrade

This new to me computer will not let me upgrade to 10.8.5 from 10.8.1 (fresh install). The App Store is not showing any updates.
I just purchase a used mid 2010 Mac Pro to replace my 2008 Mac Pro (It's Protools related... don't ask). The previous owner said that he had wiped the drive and had restored the computer back to the original version of Lion that the computer came with. So when I got home, I plugged in the computer and booted from a Mountain Lion USB flash drive that I had made when I had originally purchased ML for my 2008 Mac Pro.
Install seemed to go fine at first. I attempted to restore some settings from my Time Machine Backup but I kept getting a JavaApplication install error. I checked the OS and it was 10.8.1. I went to App Store app and looked for upgrades to get me back to 10.8.5 but it said there were none. I restarted and was still having the problems with the JavaApp pop up and no updates in the App Store.
I then rebooted from the USB stick and repaired permissions twice. I rebooted and while the JavaApp pop up was no longer annoyingly popping up every 2 seconds, I still was not being given the option to upgrade past 10.8.1.
Figuring that maybe something could have gone wrong with the time machine restore, I rebooted from the stick again, wiped the drive again and reinstalled again. This time I skipped the restore and left most of my info blank. I then went straight to the app store and still nothing. I tried searching for similar problems on apple forums. Found a list of preferences to trash. Tried that and nothing happened. I tried re-downloading the Mountain Lion installer but I can't tell if it's the latest version or the version I bought and as it is well after midnight, I am trepidatious regarding running it just to find out I'm in the same situation.
The apple support page brings me to a list of upgrades and security updates but when I click on the links there are no downloads except for the very last one for 10.8.5.
Any assistance would be greatly appreciated.
Will
Mac Pro 5,1 (2010)
2x 2.4 Quad
16 GB 1066 Ram.

You can run the 10.8.5 combo and 10.8.5 supplemental installers, instead of going through the frequently wonky App Store:
OS X Mountain Lion Update v10.8.5 (Combo)
OS X Mountain Lion 10.8.5 Supplemental Update
Apple - Support - Downloads

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