I did not see a .limewire preferences folder, but I did try and download one of those MagnetMix files. I was getting 615 Kb/s to 685 Kb/s while downloading from them, does that mean that people I've been previously downloading from just have slower connections than what they have listed? If so that would explain the slow download speeds.

I will try downloading from several users to see if I get different results, if users have been lying about their connection speeds I'l be able to find out by trying different files from different users.

Downloading a file from Magnetmix is a bit of a test, if you get snail speed there too then it can point to an ISP shaping bandwidth. Sounds like your speeds were pretty good!
Your prefs are probably here:
C:\Documents and Settings\your name\Application Data\LimeWire. It's a hidden folder, so you'll have to show hidden files & folders to see it!

Have you been through the link about configuring LW for best performance? It's worth a try.