I'm using AmpliTube right now and don't have any problems with noise. Although I can't monitor the sound simultaneously with the original signal cause of my Mac limitations. I usually record using an overdrive sound with a seperate cabinetulator and then go back and tweak the recorded track later. Besides.... then you can be more accurate in how you match up the sounds.
(The British Tube sound with the 2X12 cabinet is awesome.... especially when you punch in the Wah.
Just like listening to old Pink Floyd albums.)