Perhaps the issue is from the odd frame rate.
You could try Shotcut’s Covert to edit-friendly feature.
It makes a new file from your source video.
With that file start a new project, and see if it takes care of the issue.
Unless you are using the timeline you are not going to see “Output”. Without screenshots, it’s hard at time to guess what is going on. More than likely you have the same odd frame rate video as your source as you left the Video Mode in Automatic.
I’m guessing if you ran your source file through Media Info, it will show you have a variable frame rate. Sometimes Shotcut will show this if it is variable, but not all of the time.
I also don’t know if you changed any settings when exporting, or if you just left everything as default. If everything was export as default settings, it would have taken on the source video frame rate, although not sure if Shotcut produces a variable frame rate video (if the source is variable frame rate).