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I was looking through the 'help' index on sonar, and it suggested the I/O buffer size might be off.
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This is the same thing as latency. Increasing the buffer increases latency and vice versa.
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The thing that has me nervous is that I used to record on Cakewalk Pro Audio 9 on this machine with no problems. Now I get the clicking and popping even when I use Pro Audio 9. Of course, this is after upgrading my mics, interface and software. So that's why I'm worried it's the interface.
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Well, it's definitely the interface and, more importantly, how that interface works within your system. I'd make sure that you are using the latest drivers. I'd also make sure that there are no chipset issues in your computer conflicting with your audio interface.
I'd also make sure you aren't overworking your CPU.
I'm also assuming you've done the old "restart computer 3 times" trick. This solves more problems than it should.
Brandon