This sounds really strange and could be a bad sector in your harddrive, about being hacked, most email companys have a software that will tell you when you log in to your email that your email as been logged in on other computers while your on, I know this because I've been hacked via gmail and gmail told me as I logged in that my email was being used else where and someone had access to it, so I think they'd alarm you..
Lets do some tests shall we to see if the harddrive is ok.. could be the oprating system, maybe a corrupted file which commenly causes freezes, also you could be correct about a hidden software in the background..
Goto Start, goto run, or alternatively press windows key and R key and run command will prompt.. type CMD and press enter, you should see a black screen appear, in the command prompt you need to type CHKDSK /R this will cheak your harddrive for errors, if it asks for admin rights, just search command prompt on your windows and right click and 'run as admin' and then repeat above..
If no problems found try downloading a program called:
CCleaner - Download CCleaner 3.12.1572 - FileHippo.com
Top right corner download and install..
After this clean the computer with CCleaner and then click registry in CCleaner and give it a fix issues in registry (scan computer)
Have it fix all issues, this hopefully will fix the computer as you could have a few bad .dll files and hopefully CCleaner fixes it.
Get back to me please if this hasn't been fixed or if it has please post anyway so google searches can get this info and have it solved from others also