Okay, here's what happened in detail.

I installed Bitcoin on C:/ with a normal installation. I made several transactions to and from the address generated by that original wallet.

Later I decided I wanted to run Bitcoin exclusively from a flash drive for security's sake. I copied the files from the data folder in Windows' Application Data, including the wallet, and pasted it in the Bitcoin folder on the flash drive.

Since then I have been running Bitcoin with the switch -datadir=[folder on flash drive] from a shortcut.

After the trouble started I uninstalled Bitcoin and installed the newer version of the client, saving only my wallet and the shortcut.

Currently, I'm running the program with the switches -datadir and -rescan. It's sitting on 8 connections and 114138 blocks. It's adding blocks VERY slowly, but the connections haven't changed in about an hour.