Nathan,
You're not imagining it. The Blue sub has a huge number of zero value pixels.
I presume you haven't calibrated the Blue sub? If you had a problem with the master bias or dark it could possibly cause something like this to happen.
Have you set the gain and offset for your QHY9? A bad offset could probably cause a problem like this too. It's a long time since I did this for my QHY12 and I don't really remember the details, but this might help:
http://www.cool.id.au/astronomy/Neb_...d%20Offset.pdf
Cheers,
Rick.