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You probably know this, but CR2 files are about as opposite to JPEGS as you can get. PS can load CR2 files, but that never happens, because calibration/aligning and stacking is done in an astro app well before PS, so you would never load an astro CR2 into PS directly.
Theoretically, stacking alone doesnt care what the file format is in, it works the same, but you wouldnt normally would be stacking CR2, it gets converted to TIFF or FITS before that. (I dont know if any astro apps stack CR2s anyway.).
I dont know about DSS, but IP decodes CR2 and converts to tiff or fits before stacking, so they are the formats used to export to PS.
Its not essentiall that the astro app reads CR2 really, you can use the Canon prog that comes with the cam to convert to tiff first, no loss in data, tiff is 16bit, non-compressing.
Just forget JPEG altogether if you move to CR2 raws.
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