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One thing I've picked up from random threads around the interweb is that the output you get from grabbing the image through the ZWO SDK and via the ASCOM driver may not be same...although I haven't tested this, since I use the ASCOM driver exclusively (so far).
The end result could be that the calibration frames don't match if you recorded lights using something like SharpCap (that can actually use the SDK or the ASCOM driver - a good place to test!) but generate your darks using an ASCOM driven program, like APT or SGP. Not sure why you would want to do that, but it's something to be aware of.
Like I said, I haven't tested this myself so take with a cup full of salt...
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