I'd try unchecking inverse telecine, disabling 3:2 pulldown on playback, and rendering out the crawl at 29.97fps, and see if you still have the same problem. If not, then it's probably due to being incorrectly inverse telecined. I don't know how (or if it is at all) intelligent the TMGPEnc inverse telecine is - does it compare frames or fields to work out which one to drop, or does it just drop every fifth one regardless?