I don't remember what the file structure is supposed to be like, but shouldn't there be a Users folder in C:/? I don't see one. I can type C:/Users in the navigation bar and it will take me there. But then all I see is a Default.migrated and a Public folders. Where's the named user account that I'm logged in on?
Unless you have changed the location of your user folder, it should be under C:/Users. Type %HOMEPATH% in the navigation bar and see where it takes you. If the folder is under C:/Users but hidden, it's possible that the attributes of the folder and the subfolders and files in it got jacked up somehow, and that this is causing weirdness with your files and settings. If so, you may have to read up on the ATTRIB command to reset attributes. I had an issue a while back in which I had to do this, but unfortunately I can't remember what the issue was. (Stupid old brain!)
There's something screwed up going on there. I type your %HOMEPATH% and it does indeed take me to my user folder. BUT it's 'empty,' unless you click on properties, in which case it has 12gb of stuff in it. The filepath reads like it should C:/Users/'my username' but if I travel to the actual C:/Users directory, my user folder is nowhere to be found, in spite of properties 'hidden' files box being checked. I haven't a clue how any of this happened unless the Windows update just borked all of it for no apparent reason.
Wait a minute...that shouldn't be flagged as 'hidden'! That's my problem! Wtf, windows?
That was it! Somehow my user folder got flagged as hidden and that's where all these problems came from, even the start menu not properly linking to things like Control Panel. Such an odd issue, and no idea how it came to be. Thanks again everybody for the help though! I never would have figured this out without that %HOMEPATH% command.