I am willing to bet you are experiencing problems with the computers ability to get to recorded information to the hard drive.
If you are recording your projects to RAM, then when your RAM fills up, it must dump the contained information to a temporary file on the hard drive so that the RAM is free for more information. This WILL cause problems in all but the very fastest of systems, and even in those.
First off, verify that you are recording to Hard Drive. You software will have a setting somewhere that will give you this option. Next, make sure that you are not running screen savers, or any auto something or another programs while you are recording. This could include also any anto virus software if you are using any. They scan new files before they allow it to go to hard drive. Next, verify that you don't have something like a 1000rpm hard drive or something (1000rpm is an exageration, but you should have at least a 5400rpm UDMA 33). If the hard drive spins too slow, that will lead to problems.
I am sure that there are a few other things that could contribute to "popping" sounds while recording.
Tell me though, if you rip a song from a CD, does it pop too?
Ed