Windows 7 (64 bit)- sudden slow start up times

Hi everyone

I'm having some problems with Windows 7 Home Premium 64 bit, on my Sony Vaio VPCEB2C5E. I got my Sony Vaio laptop in November 2010 so it's not too old. Upon booting up Windows 7 on the 15th Feb 2011, i noticed the time it took windows to be functional had drastically increased from the night before when it was loaded. I hadn't installed any programs on it over the past several weeks, and about the only things i had running were Google Chrome (watching videos on Youtube), Minecraft and MSN Messenger.

Now every time when i boot up and I've logged in, i have to wait 5-10 minutes or so before i can even start to load programs or connect to a network, otherwise windows seems to not load the program i double clicked and seems to stop loading anything, but the mouse and keyboard still work and a hard shut down (holding down the power button) is required.
I tested Ubuntu on the Vaio and it seems to load fine, i have even tested out Windows 98 which also works fine (thus eliminating the possibility of a faulty Hard Drive), it's just windows 7 which had suddenly got a slow load up time for me. Once i have waited a long time windows seems to work fine and i can run and open everything i want, as quick as i would normally do prior to this problem.
A friend suggested it might be some kind of driver not being loaded from the "Kernal" in Windows 7 or something. Can anyone help me? :)

Hi again NoN, I've tried doing the System file checker and the hot fix didn't seem to help either. However i did a scan of my PC using Kaspersky Internet Security 2011 and found a Trojan in the Java folder in User apps, Kaspersky removed it and found no other viruses in it's complete scan of the Hard Drive.

The problem now not only affects the booting, but also random lock ups occur and i can still move the mouse around the screen, but nothing else. usually this happens when i try to open a program or close a window, even if it's just windows explorer, the only way to get it working again is to reset the laptop. Could it be the virus that did something, or maybe it could even be Hardware (but the laptop isn't even 5 months old), I'm starting to get a bit worried.