multi-tracking to the system disk is always risky - could be that it's just bottle-necked on the way in.
I used to get this when my buffers were set too low, if you don't need to monitor stuff with low latency whilst recording (like you do when overdubbing etc...) then ramp your buffer up - this is why I like to record bands 'live', they listen to each other in the room, instead of an audio interface.