Hi Harry,
There should be no problem at all with scale differences; StarAlignment can deal with them (within certain limits, of course).
Hot pixels can indeed be a problem. You can try increasing the number of noise layers to filter hot pixels out. However, as Sander has said, you can upload your images and I'll be glad to take a look at them. You can upload them (preferably packed as a single zip file) to our anonymous ftp server. You already have used our ftp before, or am I wrong?
StarAlignment is one of our "leading ships" so I'm always interested in improving it by testing difficult cases.