I want to know if my windows is genuine though it shows that it is.

None. Also to mention, I used TDSSKiller and ESET Online Scan. This problem started after I used MGADiag tool for the first time.

It sounds to me like a race condition - something is blocking the normal operation of the Software Protection Services, resulting in them flagging the system as non-genuine. once that condition no longer pertains, then forcing the system to re-evaluate the license corrects it, and all is well again.
It's nigh on impossible to isolate the cause of this type of thing, but it usually goes away after a few days as the system re-optimises itself.
Have a look in the event viewer and see if you can see any related incidents there - it may give us some clues.

Have you managed to get sfc /scannow to work? That seems symptomatic of the problem...Noel?

...must admit I didn't go back that far in the thread
Good point, though, since if SFC isn't working it points to some fairly major system problems.

Sorry for replying late. My SFC worked but it said that another repair is in progress (the genuine message which said it had to repair something). I've already uploaded CBS.log to my skydrive. You can check previous posts to find out the upload. I checked my CBS.log and it had something to do with themeui. I have got Windows 7 Home Basic which has no aero transparency so I used a tool called Aero Unlocker (available at winaero.com) . I think it tampered with themeui to unlock transparency and after I used MGADiag tool, it thought that windows wasn't genuine. My bad. Thanks to all of you who helped me on this. Currently, I have got no genuine messages but I'll post back if anything bad happens. Do you think I can use aero unlocker again without getting messages?

It's unlikely - it almost certainly affects items checked by the Software Protection Service, and that's what causes the flag.