Freezes and Taskbar Problems

Hi, so i've been having many problems with my computer ever since I factory reset it due to a virus.
So the problem is that when I click a program on my taskbar, it does not pop up and it just stays minimized. It happens really often too. Usually I would need to click two to five time for it to pop up, but sometimes it still choses to stay minimized. The only sure way of maximizing it is hovering my mouse over the application, waiting for the preview to pop up, then right clicking the image and then maximize. Also, another problem is some that some of my windowed applications become unresponsive for about half a second the majority of the times I click on it. For example when I play solitaire, more than half the times I click on it, it becomes unresponsive half a second and resumes. Same for many other things. When I play games with a dedicated full screen mode, everything runs smoothly, but when I put it on windowed, more than 50% of the clicks will make the program unresponsive for a fraction of a second.
Thank you for your time and hope to hear from someone soon!

 

when it freezes, hit control-alt-del and go to task manager and check the process tab for what process is hogging the CPU. IF you can't figure how to fix it from there then get back to us with what's using up your CPU time and we may be able to figure out something to try.

It could be that your system is just too slow and needs time to get done with something to be able to do another.

If problem still persists try
http://www.techyv.com/questions/windows-7-taskbar-transparency-not-working

 

My CPU usage was about 1-4% when I checked while playing solitaire and nothing was hogging the CPU usage
But I was still experiencing the not responding
It happens when I click on the program, it stops responding for less than half a second and then works fine again but happens nonstop
And I looked at the article, my computers base score is 6.8
I don't believe its my computer being slow because I run a Solid State Drive, but thanks!

 

Since you have done the factory reset have you updated drivers and windows?

 

Yeah all of my video graphics and sound drivers are up to date and I installed all of the windows update things

 

Try in Safe Mode by tapping F8 on startup and see if it acts the same

 

Everything is working fine in safe mode, but then again a lot of programs aren't opening in safe mode, like for example the programs which usually freeze are games but I can't test any of them in safe mode

 

http://support.microsoft.com/kb/929135
maybe give this a look since things seems to work better in safe mode. Possible 3rd party software conflict

 

After stopping all of my 3d party services and leaving the all the Microsoft ones on, all of the problems are reduced dramatically but they still reappear once in a while
So should I try disabling some of the microsoft services too until I find the troubled one? Because all of my windows updates are up to date

Edit: Actually I lied, I turned all 3d party services off and all the problems came back again