I think that the problem reported by Jo it's a real one. I've seen it before. Some times I use the align module with the guide scope and then, when I change to the main telescope to generate accurate WCS entries on the main image, so I can fine tunning the framing of a target. When I latter select again the guider, sometimes the FL on the final images is from the guidescope,
Jo, do you remember if you have been changing between guidescope and main telescope?