Hi Jules,
On my machine, at least, that message comes up as a "Warning", and just tells you that PI determined that applying the dark frame to the light frame made the resulting frame noisier, so the dark wasn't applied and the light frame was left as is. Since its a warning, I don't worry about it - much. I DO notice that if you have a LOT of light frames that generate this Warning during dark application, the resultant stack of lights after integration seem more coarse in appearance.
I did find that these warnings more frequently show up when the duration of the dark frame is REALLY different from the light, ie. a 600s dark applied to a 3s light (a bunch of 3s images of C2011/L4 in near twilight recently). I did some 180s darks just to test my thinking, and when applied to the 3s light frames the Warning didn't show up and the darks were applied. The resulting stack of integrated light frames looked better for having the darks applied... but that may be just my imagination.
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Don't know if that helps or not.
Rod