i've never tried to upload a fits file to astrometry... there is of course no way to specify the origin of a fits file (meaning, which corner of the image is byte 0), so maybe that's what astrometry was complaining about. sounds consistent with the flipping you observed.
anyway glad to hear it's working right. GMM is really sensitive to brightness differences at the overlaps and so i guess that 'extra' stuff was really messing it up.
a blind solver would be good - i think the astrometry.net source is open source so there's something to build on. i remember hearing that the algorithm shares some similarities with how shazam/soundhound identify music.
rob