My computer has a weird thing going on. When windows starts up I see the System process using 100% of the CPU for about 2-3 minutes and then it subsides. I wonder why this happens. I'm sure my computer is virus and spyware free. And I don't face no other problems once this 2-3 minutes pass by. Any idea why this happens?
Install Process Explorer, and make sure it runs at startup. It keeps a history of recent processor usage, and tells you which programs were taxing the CPU most at any given time (mouse over the CPU history and a tooltip appears identifying the CPU hog at that time).
If you don't find the culprit in Start, All Programs, Startup Items then you may want to check for other startup items by using msconfig.
Click on Start, Run (may be different in vista) type in msconfig, press ok, and click on the startup tab at the top.
These are all of the programs that start with your machine. It is safe to disable all of these items but you shouldn't have to. If you notice the name of a program you don't use anymore uncheck it here. If something seems fishy google it to find out what it does and uncheck it if you want. When you're finished cleaning these out press ok and restart.
Autoruns (from Sysinternals) can be an eye-opener too.
Try sysinternals process explorer, maybe you get more information, what exactly
happening after start.
This may be caused by a "zombie" print job (that is, one which could not be successfully printed for some reason, but which was not automatically deleted by the print spooler). When this happens, the system will continue trying to print the document over and over, spiking your System process. Check to see if a document is stuck in your print queue, and if so, delete it.
If it's your system process that's using that much cpu it can be the cause of a bad driver or your antivirus software.
Do you get the same problem if you Windows start in safe mode?
You can use msconfig to disable most autostart entries.
Start, type msconfig and press enter. Go to the services tab and mark hide all Microsoft services, (Make sure you did not miss the previous step, your machine will likely not boot)press disable all. Go to the startup tab and press disable all. Click Ok and reboot. Does it work better now?
If it's working better then you might need to try out the autostart apps one by one to figure out which one is causing your issue.
If it's not working any better I would suggest checking for new drivers and uninstall any antivirus/firewall software since you cannot disable them reliably.