Hello ollie,
Thank you for your post.
I've tried to used
the latest beta version and it joined these two files sucessfully without "unmatched" content notification.
Please let us know what operation you have tried to use, what task you need to be done? Was it
Join Manager or have you tried to used e.g. "
Save all fragment as" option from the menu opens after the right mouse clicking on the timeline?
If you would like these fragments to be saved after they were selected on the timeline to the single file, then you need to click the "Save" button.