Background: I had a working system with no issues until last week. I made the mistake of installing Windows 10 and it caused a ton of issues, so I decided to wipe my system clean and reinstall Win 8.1 (full clean install, I think I actually repartitioned the hard drive). Anyhow, after installing 8.1, I installed all updates and all my hardware was automatically recognized and everything was identified in the Device Manager. I went ahead and updated the Display Adapter driver just to be sure. One issue that was already happening at that point is I get a "Can't change the size of items on this Display" error at the bottom of the Display control panel page. I also have a reduced subset of Power Options available than usual (Dim the display isn't available for instance)

Problem: The real issue started when I applied a theme to my desktop, I did what I always do, patch using UXTheme and apply a visual style (that I've been using for over a year without issues). As soon as I did that, I lost access to Computer Management, including the Device Manager and Disk Management tools. Also, certain application started crashing or not starting up at all (Matlab, which has a java-based GUI won't start at all for example, not sure what the connection is there, since other java-based programs run fine). I should note that if I change the theme back to any windows theme (non-third-party), Computer Management is back and I can start matlab, so it's not patching the system files that's doing it, it's the particular theme being used when the tool/application is launched. I've tried multiple custom themes and they all had the same behavior.

TL;DR Version: Formatted laptop, have missing options in Power Options and Display, installed 3rd party theme --> caused system tools not to open and some programs (Matlab) --> system tools and Matlab work fine if I switch the theme back

I've never seen this sort of behavior before, not even sure where to start. Computer Management and Matlab are obviously looking for something that is available in the default windows theme engine but not in custom themes, but I have no idea what that might be.