[...] but after playing for a little bit my computer always restarts for no reason! I gave up on playing it for awhile after messing with some of the game settings, but I just tried to run it again today, my computer suddenly restarted right at the start of the game
Looks like a driver or system issue to me. Which OS are you using? Graphics card? Aquaria version?
Another possibility is that your system is overheating, but if it happens right after starting the game it's less likely.
If you're using windows, first disable autoreboot on bluescreen. If it bluescreens that may at least give you some info of what is wrong.
To be sure your system isn't overheating, run this for 10-15 mins:
http://www.ozone3d.net/benchmarks/fur/If your machine doesn't reboot or produce garbage in that time, it's ok.
My saves were all deleted for some reason.
I assume you run Vista or win7.
First, Aquaria doesn't delete saves (there is no such function in the code).
Some win7/vista virtual file system compatibility layer bullshit likes to put them somewhere into hard to find folders in your user profile directories; was discussed in this topic:
http://www.bit-blot.com/forum/index.php?topic=464.0(I still use XP so I can't help you with this)