Well, some more unexpected clear skies - did some more testing in the garden and definitely had dark frames in place and no change in the noise.
Even altering the gain had little impact on the noise tbh and I fiddled with various other settings in the driver but no real luck although changing the white balance seemed to be having some effect but fairly minimal.
However you can make out your target star from the noise (on the unit we have anyway) and I got the mount dialled in to what it told me was 1arcminute of alignment error so it is certainly viable to use the ipolar with the alignment module.
I can only throw wild guesses as to what is happening but it really looks like it's not subtracting the dark frame. Is it possible that because the refresh exposure has to be so low it doesn't have time to process it ?