What is your operating system?
What is your Shotcut version (see Help > About Shotcut)?
Can you repeat the problem? If so, what are the steps?
Yes. If I load an image sequence (or video) and add audio to it and export at the normal project framerate, everything works. If I half the framerate (for export, not the project framerate), the video is exported correctly at half framreate, but no audio and the resulting file has seeking errors and creates unpredictable seeking behaviour (varying from player to player).
Edit: Ok, this only seems to happen when trying to use b-frames… for some reason (HEVC codec with nvenc…)