Well, it seems I solved it just now. For some reason it boiled down to my registry tweaks alone. I was loading them via the cmdlines.txt and a batch file. I found that when I removed them the OS operated and installed MSI apps normally. When I put them back in the cmdlines file it acted up all over again. I then tried loading them one by one after the OS installed to see which caused the problem, but nothing went wrong. So I moved them to the runonce on first boot up and it now will install all the 3rd party apps correctly and add my tweaks as well. Not sure why this change fixed it, but it did. If anyone has any ideas or suggestions, I'd love to hear them! For now I will leave them in the runonce. Thanks!