Hi,
I would suggest that to help the transcription identify different speakers, that before starting the transcription, there would be options to identify the number of speakers (as another poster suggested), their names/pseudonyms, as well as identifying a passage of speech by each speaker to help the software to differentiate between different people. I recently had an interview where the software interpreted the participant's voice as 5 different speaker (I am male, the participant was female, and our voices are quite dissimilar), and would identify a new speaker every 5-10 words she spoke, which added a lot of time editing the transcript to make it be usable. I know this won't eliminate all issues with identifying speakers, but I imagine it would reduce errors by a lot.
Thanks!