OS X Not Saving Changes On Shutdown

I have a 27" iMac that I bought in February. Last night I installed an SSD into the Optical Drive slot and now the weirdest thing is happening.

I have OS X installed on the drive, and it boots no problem, but, oddly, anything I do isn't saved on shutdown.

Example:

Example 2:

It's like it's reverting back to some random version of the OS ; I don't have anything like Deep Freeze running, though, nor is this drive set up for Time Machine. It has my MobileMe freaking the heck out too, it keeps saying it needs to rebuild x, y, or z when I log in. Really weird!!

I've repaired disk and permissions I... I've got nothing. This is so weird!

- Kira

 

Wow, really a stumper, eh? Well I'm reinstalling the OS to see if that helps >.x

 

I have since reinstalled the OS, however I do recall downloading something about that size the first time I had thought it fixed. I waited until it had finished, then restarted the OS and it reverted as if I'd never downloaded the thing in the first place. I didn't think to check the HDD usage though. What sort of problem are you thinking towards?