Thanks for your post- so, to confirm, you have NOT selected "force column order", and SQL Compare shows the table as different still, is that right?
If there are other differences, then the table will be seen as different, and because of the way the display works, it'll still show the column order being different too (other differences could be extended properties, index names etc etc).
If you can't spot the difference, then it may be that it's not visible, or there's perhaps something else strange going on, in which case, please email the file from the script folder and also the table definition from the database (script it out to a CREATE TO window) and send over to firstname.lastname@example.org
so we can look into it. If you do this, please quote F0062272 in the subject line.