Just some input on this...I have the same problem and it is most disturbing and I can tell that this problem does not happen all time...I am using only one sound card, M-Audio Audiophile 2496
When I run into this clicking issue, and there is no telling when it going to start, it only occurs during the track when I play my keyboard or record a vocal, anotherwords when I am actually sending input, if I do not play there is no clicking on the track even if I am recording until I hit a note...
What I have been doing is when I run into the problem is open a new project if I don't have other tracks recorded or record on a different track and it seems that the clicking stops...
It is funny because if I go back to the track that the clicking was on and try to record on the track the clicking or static sound is there again when I hit notes...
Now this is not a fix, but a workaround for me...I will be watching to see if there is any additional advice here that can help me resolve this problem as well...