How is automated tone transcription affected by the choice of transcription orthography? In this paper we present a range of experiments that indicate that, even when the tonal repre- sentations are kept the same, the way vowels and consonants are transcribed can affect tonal character outputs. Our results also indicate that using a Language Model (LM) for decoding can mitigate problems with tonal outputs, but tones remain the most difficult part of the tran- scription. In doing this we also present the first Automatic Speech Recognition (ASR) models for the Baima language, spoken in Sichuan and Gansu, China. We hope to use these models to contribute to ongoing documentation efforts.