Unknown Operating System Problem (See attatched image)

So the other day I got a pain in the butt virus (GFW I think it was) http://www.sophos.com/en-us/threat-center/threat-analyses/viruses-and-spyware/W32~Rbot-GFW.aspx . Well I ran Malware-Bytes and got the infected files off. And I started up the computer again and it looked very weird. So I went looking to see if all my files were there and they were all hidden. Fixed that but it still looks weird. So I did a repair install of Windows and it still looks the same. My next step is a complete reinstall of Windows (waiting on an external I just ordered). I was wondering if I need to go that far or if there is a setting somewhere that is doing this.

Any help is appreciated, Thanks.

P.S. The clock/ T is rainmeter. They are supposed to be there.

Did you attempt a system restore? How did you get a virus ? Did you download something and not scan it with MSE or MB before you opened it ?

The virus deleted my restore points. I've been asking myself how I got the virus too. I was playin a flash game and listening to music when it tweaked out said my hard drive went bad and threw up 20 some popups about my drive. Restarted my computer and it wouldn't start. Had to do a bootmbr repair to run even safe mode. And I download lots of things and not scan them sadly ^^ but not on this occasion. Thanks for the quick reply.

You tried to change the theme and nothing happened ?

Just tried. Didn't help. Although I'm not sure it would help with the start menu at all. The 2 main problems the picture was showing were the expanded (not sure how to phrase it) task bar icons and the emptyness of the start menu. Side note Aero is still running.

Do you have a recovery partition ? If not go for the clean install.

Have you scanned it with MSEssentials ?

Clean Reinstall - Factory OEM Windows 7

I do but its empty for some reason (the virus didn't do that it hasn't been there since I installed windows in the first place) . So I'm off to do a clean install (tomorrow when my drive gets in) thanks for your help.

Figured it out after some more thought out searches (at first I couldn't think of the right words to search. It was all very simple actually. All I had to do was right click the toolbar and go into properties. It brought up a menu that let me customize the entire toolbar which, in addition to returning it to normal, allowed me to customize it more than it already was.

I'm going to do it because you look qualified to tell me what to do, but what does running it 3 times do?