Thanks for the detailed description, and for the songs what you sent us in email.
I found what cause the issue.
When you change the target device (uTrack24 or LP-16) not all parameters saved properly.
I can offer you one workaround until we release the new version (really soon)
Please close and reopen the uTool when you change the target device, after that the output file will have no this issue.
We are sorry for the inconveniences.