@gollum,
Window system it would seem now what version?
Start the task manager at start up so you can see the total cpu and memory being used and the tasks being run and if a program is not responsing.
Suggest you allow it to sit for a time to see if if come back to you at some point and if so then look at the event system viewer to see if errors are being reported.
Go to run command on the start menu and type msconfig and see what programs are set to run on startup and disable one after another until the program go away.