Hi Ken, Nick from wet hampshire here.
I had the exact same problem with the scanner calibration plate not lining up.
The quick fix is turn the machine off (Or i think click on the Flux symbol top left of the user screen. this will allow you to change from each mode i.e. laser engraver, scanner, printer etc)
once this machine is off, you can freely rotate the scan platform to align the slot so it is parallel.
I hope that this helps.
Happy Storm Brian.