Phil,
I would first do a bit more testing. But anytime you take a CCD or CMOS for that matter past about 20 seconds, you are pushing that chip a bit and if you have heat and humidity in the shooting environment, you will get more possible problems.
Traditional stuck pixels, tend to be red green or blue and I also believe that most of the dark frame algorithms are looking for that. Where as a pure white may be overlooked.
I do a lot of night photography with both Canon and Nikon (CMOS) but have shot with a P45+ for up to 1 hour. The Canon 6D has a known issue with white spots, these however are a bit larger than the single pixel size you are talking about. They will show up after about 1 hour of use and once there stay there for the rest of the night. However as they are not numerous it's very easy to map them out later on in LR or C1.
The D800 on the other hand gets thousands of the single pixel whilte spots on hot or humid nights. I wrote a article on my website about this.
http://photosofarkansas.com/2013/08/02/d800-reticulation-issues-during-night-photography-white-dot-problems/I mainly shoot in stacks, so I can't use long noise reduction (dark frame) with Nikon or Canon as my stacks can run as long as 3 minutes each. The dark frame will create a gap in the star trails that you may or may not be able to get out. To their credit Canon does buffer some of this but the buffer issue creates other problems. Nikon works just like your Pentax or Phase One, if turned on, the camera is dedicated to the dark frame as the next exposure.
The Nikon white dots will happen on any warm or humid or both night, which in Arkansas are common.
The best tool I have found to remove them without massive noise reduction destruction to the rest of the image is the "single Pixel noise reduction" slider in C1. It can to an amazing job. I realize that the 645D image (raw) can't be opened by Phase One, (another issue C1 should address if they want to be considered a "global raw tool" like LR). However you might be able to save these raw conversions as a tiff and then open the tiff in C1 to use the single pixel noise reduction tool. (You can download C1 as a trial for 60 days).
You should also try to turn on the long exposure noise reduction on the 645D just as a test to see if it can see these white dots and map them out in the dark frame. Each company handles this algorithm differently.
I don't think anything is wrong with the camera at all, it's just the whole issue of long exposures on digital equipment.
Paul
