First comes to mind:
This has nothing to do with PC resources.
How are you monitoring during recording? Not with loudspeakers? If the loud noise starts right when you hit the Record button (before you've played a sound), it must be some sort of routing/feedback problem, i.e. the sound of either the first recorded track or the one you've armed for recording can loop out and back in.
(Unfinished thought:Could, say, leaving the Input Echo of the first track on cause something like this? )