I am experienceing the same thing after updating to X2a, I posted:
http://forum.cakewalk.com/tm.aspx?m=2743032 a days ago. Last night I found that if I froze BFD2 it stopped while at 128K buffer size, didn't have to do this previously. As I increase buffer size, the pops and cracks go away, basically the only time I get them is at 128k buffer size. Which is what I track at because there is no latency. So I have been freezing several tracks while tracking, which is inconvenient and didn't have to do that before. Another interesting thing, I restored back to X2 using system restore and the pops and cracks are still there. The only change which was made was the X2a update. I did go back thru the services and shut off / disabled anything that I thought was not required for the machine to operate. however Windows 7 has so many services, Its hard to determine what is required for the machine to run. side note: I wish there was a version of windows available which is optimized for recording or at least a bare bones version with the most minimal services / apps for a machine to operate. I probably didn't help out any, but just letting you know I am experiencing that same issue.