I have no idea how this happened, I scanned both my Internal and External HD's and both are malware free. The data in my External HD was corrupted and I ran several disc checks to see if it could find any errors, but no bad volumes were detected.
Whenever I try to access my External HD, I get a warning from ThreatFire tagging it as a serious threat for trying to use the process Shell32.dll which leads to my settings. If I allow the process to continue, the HD won't open and then it says my firewall has been disabled. If I kill and quarantine the process, then my computer does some sort of strange restart where it freezes for about a minute or then the screen goes black and comes back on again.
After all this happens, the next I boot my computer, the system treats it as if a crash happens, and if I try to boot with the Windows default settings, then it gets stuck at the loading screen, if I boot with Last Known Settings That Worked, then my computer runs fine. Nothing works off of my External HD anymore, which is about 150GB of music.