Hi Jan,
I've seen this a few times, and it almost always is that one of your selections is including a bit of where the laser is moving back to the reference materials. Because the selection includes these x, y values, the image space becomes much larger and takes longer to process.
I would check to make sure that no selections for the image scan lines extend beyond the data (even a point or two when the laser is moving quite fast to return to the RMs can produce this effect).
If you can't easily find it, I can explain some additional steps to help highlight where it is happening, but it does require a bit of python, so please let us know if you need the additional steps.
Kind regards,
Bence