Good idea. I'll give it a try the next time it happens.
Did you resolve this problem? It sounds like a classic mismatch of your sample rate between your session setup and your interface. Also, sometimes a single, unauthorized plug-in can be the source of a mystery click. Many of the manufacturers will put in a "watermark" of some type of noise or another to their plug-in to mess up your mix, until you have properly authorized a plug in. You may have paid for it and authorized it even with a prior version of the software, but upgraded it, and just not re-registered it correctly somehow. It's just a hunch. I've had that happen before, and had intermittent noise that took me a while to isolate. If checking the sample rate settings on the session and hardware to match doesn't fix the issue, then work through each track and isolate the plug-in's to check for the source of the pops and clicks. If they're random in nature, you'll find them somewhere. It's one of those two sources, I'd be willing to bet.
The suggested solution by Robert might eliminate (or might have eliminated) the problem by default because you may have created the new session with a setup at a matching sample rate, and then converted the old sound files correctly. So that's a workaround for sure.
Let me know if this isn't solved, though it's clearly a few months late. I just wanted to reply in case others see this post and are having a similar issue. Especially if the clicks aren't recorded and are occurring randomly. But I'd think 90% of the time with the situation described, it's a clock mismatch issue, based in the sample rate being wrong.