What is your operating system?
Windows 11 Pro; build 22621.2715
What is your Shotcut version (see Help > About Shotcut)?
Can you repeat the problem? If so, what are the steps?
I have my main cut saved as an MLT and have loaded that MLT into a new project. In the new project the audio waveform is misaligned.
In below screenshot you can see the audio peak meter showing almost silence - as it is the end of my intro clip - yet the waveform seems to show as if the playhead is still in the middle of the intro.