Straightening panoramas made from .cr2 RAW files

[apaul34208]

I'm having trouble straightening panoramas stitched from Canon's RAW file format, cr2 files. I can get them to look good within the straightening tool, but when I hit save result, the panorama reverts to the original orientation. Basically it looks straight after setting the 2 lines with the straightening tool, but it will not save the result.