[Jack Simth]

Partially depends on your OS and system specs, but....
Essentially, it means that something is hogging recources - perhaps a system routine, perhaps a program - in a relatively exclusive mannor.

Check the Task Manager when everything's fine, write down what's in it, then check it again while paused (if you can); what's new? Might be the problem.

Try Alt-Tabbing when it pauses (hold down Alt) I once found a program that had come installed on my machine which was trying to call home for an update... I eventually found out it was a program that was no longer supported due to security issues, and removed it. Was a pain anyway, as it would interrupt me in the middle of typing and change the focus to the desktop.

Edit: Also, get your machine scanned for viruses & spyware. Either could cause such a phenominon