It's probably not Amplitube in general because I also get that noise in ReValver.
I have a Realtex AC97 Audio card. Probably not the best one in the world, but it works. What I do is use the front input and in the recording control, I just select CD/Video in which is the front one. Maybe it's the noise from the cord being beat up. It's just a 1/8" cord converting to one 1/4" adapter and neither one is in the best shape.
EDIT: It can't be the cord... blah I don't know what it is.
"Most of the songs I write are all love ballads and things
having to do with sadness and torture and pain:
at the same time it's frivolous and tongue in cheek. That's
basically my whole nature, I guess."
- Freddie Mercury