I figured out what was wrong. Although I don't know why it happened in the first place nor do I know what fixed it.
I decided to try on my laptop to see if I could reproduce the problem. Clean install, smooth patching, and I set up the framework identically. All of that however, is not what fixed it. After finding that my settings correctly showed in the game on my laptop, I decided to compare the files on the two computers to look for differences. When I opened the aweconfig.package with notepad on my desktop computer, I found that everything in the file was just one long run on sentence, but when I opened the aweconfig file from the laptop, I found that it was what you would expect to see in an XML file, with line spacing and all that good stuff. Puzzled as to what caused the file on my desktop to mutate, I downloaded 4 more aweconfig files on my desk top. One in firefox using the image, one in firefox using the generate button, one in explorer using the image, and the last in explorer using the generate button. I opened all of them in notepad and they were all identical, perfect xml files. I moved one into the game, loaded up, and all my settings are there.
So, I know why it wasn't working before, the xml somehow was altered into one long line. But I don't know what caused or fixed it. Since my last post I have made no changes to my computer or any of the game files.
So, problem fixed, but mystery unsolved.
Thank you for the help. Now I'll slink back into the shadows to quietly lurk.