Sorry about the weird feeling with your trainer. I spoke with CycleOps, and I'll try to explain what's going on. If you'd prefer to discuss this over the phone, feel free to call us at 888-276-7130.
Because these trainers allow you to freewheel (like you would on a normal bicycle - ie coast), the pedals won't always have tension on them like a more "old school" trainer might. What could happen is if you're not focusing on carrying the pedaling motion through the entire stroke, you end up with a "dead spot," which, on a trainer like this, would result in a clunk when you re-apply pressure to the pedals. This shouldn't hurt the machine, but if it annoys you enough (or if you want to just work on your form), you can turn up the resistance a bit, which should help out (slowing down the pedaling cadence will help, too). If neither of these work for you, I believe they can convert the trainer to a fixed gear style, which would prevent this altogether. Let me know, and I hope it's not too late to salvage the experience, as these are really nice trainers.