Tracy,
The original IPSyn paper says that unintelligible utterances are excluded, but it doesn’t mention or discuss partially unintelligible utterances. So, I would say that either including or excluding them is a bit of a judgment call. If your transcript has enough utterances, then excluding might make sense. As the manual states, it is easy to exclude an utterance by adding the [+ ipe] postcode.
— Brian MacWhinney
Teresa Heinz Professor of Cognitive Psychology,
Language Technologies and Modern Languages, CMU