Rodd,
In answer to "what do I do?" it's pretty simple. I use the tools that work for a given image. In the case of an image full of nebulosity I simply don't use BN any more than I use Dynamic Background Extraction since you need a clean background to be able to use that effectively as well. In the latter case, I will test using ABE which works surprisingly well with lots of nebulosity and otherwise make sure I have a top notch flat master for each color to eliminate light variations that way. With background neutralization, the same applies. PI has a huge toolkit to work with but sometimes, no matter how much you like it and how much it works on other problems, a tool just doesn't work for what you are trying to fix. I love pounding on things with a hammer but rarely use one when fixing a leaky faucet.
In cases like yours, I simply use other tools. That set includes Curves Transformation, particularly the hue setting, SCNR, a touch of Histogram Transform, etc. Its in times like these where the "art" part comes a bit more to the forefront, but, in reality its all a mix of science and art anyway, even with RGB images.
And if you absolutely insist on using BN, then go with Rob's suggestion or ferret out those few clean background pixels as Geoff suggests. Just make sure you do your pre-processing to eliminate those cold pixels you are worried about (which should happen naturally since you won't be doing any BN until after calibration and image integration, so that concern is a bit of a red herring). There is a sequence and a set of tools that will fix any image. A big part of the joy of this adventure is the process of discovery in finding those solutions. That type of playing around explains why my workbook is now up to Rev41a. I find a new way of doing things with every image I process.
Good luck,
Jim