When I boot holding option, both Mac and Bootcamp partitions show up, but disappear after 2 seconds.

I recently swapped out my HDD for an SSD in my 2007 MBP. Hardware installed fine. I installed Mountain Lion from a time machine backup (of the same machine). I made the Windows partition in OSX, then installed Windows 7 on the partition it had made. In Windows, I updated Bootcamp to 3.3.
Everything seems to work fine in both OSX and Bootcamp from what I can tell. The problem is, when I boot and hold option to choose my boot drive, both drives appear and then disappear in about 2 seconds. They disappear with a "poof" animation, as if you had dragged an app off of the dock. If I'm fast enough, I can choose the boot drive before it disappears.
I tried once again reinstalling OSX from my last time machine backup (prior to the SSD swap), and the problem persists.
I thought it might have something to do with NTFS 3G and MacFuse, because I'd heard that they cause a bug where the bootcamp partition won't show up under the "startup disk" preferences pane. When I uninstalled said programs, bootcamp showed up under there startup disk options, but the problem persists.
Any ideas?

Actually, this is just getting weirder.
Disregard my edit above. Clicking once doesn't have any effect on the drives. But the drives disappear only coming off of a RESTART from OSX. If I Shut down fully, the problem is solved. Likewise, if the drives have disappeared after a restart and I am forced to turn off the computer by pressing the power button, upon boot up the drives no longer disappear (Regardless of any action I take).
It would seem that the drives are disappearing due to something during the restart process.
Okay: Here are some workflows that might shed light on the situation:
Boot to Mac -> Shut down -> Alt boot : DOES NOT DISAPPEAR
Boot to Mac -> Restart -> Alt boot: DISAPPEARS
Boot to Mac -> Shut Down -> Alt boot -> Boot to Windows -> Shutdown or restart -> Alt boot : DOES NOT DISAPPEAR
Boot to Mac -> Restart -> Alt boot & fast select -> Boot to Windows -> Shutdown or restart -> Alt boot: DISAPPEARS
Boot to Mac -> Restart -> Alt boot & disappears -> Turn power off -> alt boot: DOES NOT DISAPPEAR
So the core culprit is something to do with OSX restart. The method of shutdown during windows doesn't seem to matter.

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