Err, by being gone I mean "the entire client doesn't load, outside of a process in explorer called litecoin-qt, using 400MB of RAM, and litecoind -getinfo says that the server is not running." The problem isn't my coins being gone, it's the whole client. I can still use litecoind, but I'm lazy and prefer the gui.
I have a minute or so of delay between when the splash screen goes away and the gui shows up. How long have you waited? If you have tons of spam transactions it could be a while.
Check the debug.log, I'm not sure where it is under windows but look in the same directory as the wallet.dat file. If it is still getting written to then the process is still working and hasn't gotten around to showing the window.