Hi,
to oversimplify, the code in SharpCap first eliminates the stars from the image (wiping out any small, bright features), then eliminates the background brightness. Once you've done that, the only thing left should be the fuzzy comet, so it is (fairly) easy to find the center of it in each image and align them. If you have anything else that might look similar in view (for instance a background galaxy), it could mess things up a bit unless the comet is substantially larger/brighter than the other things.
cheers,
Robin