Trying to add phonetic transcription (and glosses) to a .WAV file

I am trying to add phonetic transcription (and glosses) to a .WAV file. I open this using the Speech Analyzer software (version 3.1), then use the Transcription Editor (function key F4). The result looks fine, but when I save it and return, the transcription is a mess. The program always offers to “correct snap alignment” for me, but whether or not I say YES to this offer, the transcription is still not properly aligned, but piled up in a corner, not neatly displayed as in the tutorial model.
I read somewhere that the program is designed for mono, and these are stereo files. Does that make them impossible to transcribe using this program? I’ve used this program for many years (currently have version 3.1 installed) and especially like the features of measuring segment length and pitch at various points. Possibly PRAAT offers the same features, but I need help learning how to use it for this purpose.


Is this still a problem?

In any case there is a revised version of Speech Analyzer at: