Aero turned off after tweaking and reboot

Guide * Windows 7 Ultimate Tweaks & Utilities *

I was recently following this thread to optimize and tweak my desktop a little bit, and even though I avoided the parts of the thread involving disabling Aero, it has disabled itself anyway and I can't seem to get it working again.

When I go to personalize, it says:
Troubleshoot problems with transparency and other Aero effects

Code:

Aero Publisher details 

Potential issues that were checked 
Mirror drivers don't support Aero effectsMirror drivers don't support Aero effects
A running program uses a mirror driver (a type of display driver) which is not compatible with the Aero desktop experience. Issue not present  
Aero effects not supported on this Windows editionAero effects not supported on this Windows edition
Some Aero features such as transparency are not included on certain Windows editions. Issue not present  
Video card driver doesn't support Aero effectsVideo card driver doesn't support Aero effects
The current video card driver isn't compatible with the Windows Display Driver Model (WDDM). Issue not present  
The Windows Experience Index has not been computedThe Windows Experience Index has not been computed
The Windows Experience Index base score measures the capability of your computer's hardware and software configuration and is one of many factors that determine whether the Aero desktop effects can run. Issue not present  

Potential issues that were checked Detection details 

 Mirror drivers don't support Aero effects Issue not present  
 
A running program uses a mirror driver (a type of display driver) which is not compatible with the Aero desktop experience. 
 
 Aero effects not supported on this Windows edition Issue not present  
 
Some Aero features such as transparency are not included on certain Windows editions. 
 
 Video card driver doesn't support Aero effects Issue not present  
 
The current video card driver isn't compatible with the Windows Display Driver Model (WDDM). 
 
 The Windows Experience Index has not been computed Issue not present  
 
The Windows Experience Index base score measures the capability of your computer's hardware and software configuration and is one of many factors that determine whether the Aero desktop effects can run.

tl;dr of the troubleshooting details, all the tests are "Issue not present"

A Guy said:

Welcome to Seven Forums alkajak. The word "tweak" raises my hackles If you have a System Restore Point from before your tweaks, I would use that 1st.

System Restore

If you run the System File Checker, it should correct this. be aware it will undo various theme mods and you will have to repatch to reapply any custom themes.

SFC /SCANNOW Command - System File Checker

A Guy

Thanks, running the file checker now, before a system restore. Will this reset all the settings I have changed for faster boot, faster SSD, registry changes, etc etc?