Glad you solved the problem. I just solved a similar problem. My sonar was making poping sounds when navigating projects and playing back. I just thought it was a latency issue, so I moved the latency all the way up and turned on caching. That didn't solve it.

After a couple weeks of fustration I finally solved it by turning off the on-board sound card in the system bios along with the other hardware I don't use (parallel port and serial ports). That cleared it right up. Now I just need to turn my latency back down!