I ran into this same problem and found a forum that seemed to explain it. It doesn’t have to do with frame rate or timecode. It has to do with how clips are flagged for the pulldown. Each time you stop recording with the camera it begins a new pulldown cadence and that’s what confuses Final Cut. Sometimes the cadence happens to stop and start at the same point, so you don’t get that error — but it’s just luck. So, the only solution I’ve found so far is to UNCHECK “Remove Advanced Pulldown” in your capture settings and then have Cinema Tools deal with cadence issues. I can’t remember where I found that post or I’d link to it here. But I hope that helps.