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I'm assuming you are stacking to reduce noise,
Have you tried stacking via file>scripts>statistics and choosing mean, adding your files and check "attemp to automatically align" ?
Reading raw files on a mac is done by Adobe camera raw I think, if you are on PC you may need an additional plug-in to read the cr2 files directly.this is just a guess though. Hope I was some help.
Goran.
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