Windows 7 - Undefinable freeze/lag

Hello everybody..

I've run into a serious issue with my comp over the last days.

Randomly (or so it seems) the whole system would just freeze. Sometimes those freezes last only a couple of seconds, sometimes up to 10 minutes.

By now, this also happens in 90-100% of the times i'm booting up. My ambilights are being fired up after about 5 minutes, internet connection is established after about 10. I can't even open up the start menu and when I do alt+ctrl+del, it would respond after about 1 minute. The screen would then say "Security options are being prepared" (literally translated from german).

I have made a few changes to my sys spec recently - after which these problems seemed to have multiplied. Yet, I've already had them before, just not so often.

It seems like something is throttling the system. Either a process in the background or the hardware itself is broken. My guess is a) the mobo or b) some issues with microsoft security essentials, since that's been giving me some weird errors in the last few days.

A little further description of the problem:
I can still move the mouse around freely, however.. when I perform too many clicks (even drawing a selection box on the desktop), the active window would grey out - be it desktop, explorer, firefox, any (windowed) game, etc. pp.
I cannot alt+tab, but I can win+tab, although I can't switch programs/windows that way. The weirdest thing is that it happens totally randomly (except for the boot-up sequence).

I checked with HijackThis, I've run CCleaner, checked computer management and turned off energy saving already, I probably googled every single webpage and/or support forums.

I'm at a loss right now, as I just can't pinpoint the problem.
Any help would be really appreciated.

Regards

Jan

edit: I just noticed, that this should have probably went into the performance forums.. maybe some mod could move it? sry for that.

Can you do a system restore back to before you made your changes?

To me your diagnoses of 'It seems like something is throttling the system' is correct.

Have you tried going into msconfig to do a selective start-up?
Have you checked Device Manager for any yellow warnings?
Have you checked Event Viewer for warnings or errors?

If you manage to start windows run TDSS Killer, and see if it finds any problems.

This sounds like some malware at work. In my sig are links to MalwareBytes and Super AntiSpyware, download both, update them and run full scans.