My set-up is similar to yours, except I'm using Garageband and a different brand pre-amp.
My guess is that the problem is with the pre-amp.
Sometimes sudden noise on my recordings is caused by interference from automobile electronics. In my headphones I can actually hear interference caused by a car idling on the street 2 floors below, and the hum and rumble ends up on the recording. The car drives away, the noise stops.
It is not vehicles, super quiet street and nothing has changed in the last year.