Apps flickering

When I bought Win 8.1 I wanted to customize something so I downloaded some freeware to change some bits (I don't recall which ones, nor what was the name of the software but it was one of those programs that enables you to change apperance and some other stuff. I am searching now, it could be "Ultimate Windows Tweaker for Windows 8" but I am not 100% sure)

Soon, I have noticed some apps started flickering. For example working in Adobe Lightroom or when alt-tabbed to Chrome, every now and then those and some other apps would flicker. They would flicker for half or more seconds, like someone is rapidly alt-tabbing apps back and forth.
Also, sometimes I am not able to alt-tab to specific software because Chrome or Photoshop are getting full attention, just like if they are on "always on top". I first need to minimize them. This bug doesnt happen often and it dissapears if I restart application, so it is not a huge deal.

I have uninstalled that software a while ago, unable to get things back as they used to be, but every day passing by my frustration grows.

Is there anything I could do beside reinstalling Windows? I dont have any backups and the problem is that 2 users are using this PC so backuping a huge amount of data would be necessary.

I have latest Win 8.1 upgrades and graphic card drivers.

Thank you for any insight.

Welcome to the forum!

No restore point before all this started? Could do a Repair install: http://www.eightforums.com/tutorials/26095-repair-install-windows-8-a.html?ltr=R

You could try Tweaking.com-Windows Repair (All In One) and just do either all or what repairs you deem necessary. I've been using it for about 3 years(on Windows 7 & 8.1) and it works if I messed something up, I only use a system image if an windows update screwed something up. My advice also is stay away from "Tweak Tools and "System Optimizers", if you can't do it thru Windows don't do it, you usually end up breaking something. Believe me I've tried all there was with Windows 7, and in the end it always made messed something up. See my signature.