Windows 8.1 Program Issues

[The Exodus]

I've recently been suffering this whole problem that I thought I had fixed not too long ago. It involves not seeming to be able to open specific applications on Windows 8. I'm not talking about the dashboard applications but actual programs, like Steam, Chrome, Skype, etc. It's extended to numerous apps but only seems to apply to those on my toolbar. I'm considering removing them to see if that works. However, this is inconsistent as it does run some applications linked to the toolbar (I'll post a list at the bottom of programs which do not seem to work so far, along with those that are connected to the toolbar but seem to function fine).

 

Originally, I thought this problem was connected to spyware that I had discovered on my computer. It seemed to fix the issue once it was gone. I'm now having this issue again and have run a security scan (I'm using F-Secure). I do know a fair bit about computers but I certainly don't have a clue what could possibly be preventing programs from opening fully. Just to clarify, they do actually run but do not appear as a window when I try to bring them forward. I see them active at the bottom but cannot use them. Does anyone have a clue as to what could be causing such a strange problem? Thanks for all help in advance.

 

Programs that run (on taskbar);

 

BizHawk corruptor

 

Windows Store

 

Internet Explorer

 

Partially working programs;

 

Steam (in Big Picture mode)

 

BitWise (in log viewer, contacts list and other miscellaneous tools)

 

Broken programs;

 

Steam (in traditional / legacy mode)

 

Skype

 

BitWise (in chat)

 

File Explorer

 

Chrome

 

Firefox

 

Addendum;

 

I'd make the assumption that there is some connection between all working programs (for one, they all seem to start up on the toolbar itself), only there doesn't seem to be any direct or clear correlation between them all as of now. I will attempt to remove some from the task bar in the hopes that this actually helps in some way. Other than that, I'm entirely lost.