hmm.. finally playing now for the first time... CD 3, track 5 so far and there is a little tick around 2:18. Is this what you've been talking about?
The last 30 seconds of the final track of disc 3 ("The X-Files End Credit (Extended #2)") was skipping on my set. I've also checked track 5 ("Little Box of Sand" from Emily) and I didn't hear a tick at 2:18 on my set.
