Have you tried a new version of Shotcut where you can hear audio frame-by-frame?
If that’s still not working, I have a possible workaround, though it is a lot of work. But, if you have a few really important audio cues… and if you can play a single track in Shotcut with no stuttering, or if you have audio separate from the video (in an audio track):
I will attempt to explain, and also, an important technique required for my suggestion has also been explained in more detail here: How to "proxy" edit with Shotcut
In a new project, open up the source video with the audio cue(s). Find the exact location of the cue, Split the video track at that moment, and apply a filter to one of the clips (perhaps a Brightness filter set to an extreme value). Do this for all of your audio cues. Then, export the video at the same framerate (can be really low quality). Rename the original source file as “filename_Original” and rename the new file to be the same as the original’s original, so that the Shotcut project uses it instead. As it’s the same length, framerate, etc., it should line up perfectly with any edits that you make, and it should be easy to see where the audio cues are now due to the visual filters applied. Then, re-rename the original file to its original name.
If you have a separate audio file, you could do something similar with an audio editor like Audacity, editing a copy of the audio file to make the places with the audio cues very obvious, perhaps selecting the word “Run!” and “Generate…”-ing white noise. Then use the same “proxy” source file swap.
Hopefully that made some kind of sense… 