Well what you say here is something is loading up in the background and you have no clue to what it is. You should be making sure that your PC is fully clean cos it seems like your pc is infected with Virus/Malware and you need to scan it for em so that it does not do more damage to the system. If possible go to windows folder in c drive while you are in Safe Mode and see if you see any suspicious files that may have been created around the time your system started to behave erratically. If you do not recognise those files then I'd try to get rid of em to see if that works. But do a full on scan on ur pc. Also back your data up if you havent done it yet. Try to get more help from Virus/Adware forums as well.
Hope this helps.
Raj