Mike the mere act of taking a long exposure will heat up the sensor from its idle temperature. I always use ICNR (in camera noise reduction) and the first light frame will have more and larger dark spots than subsequent light frames. This is due to the sensor heating up slowly during the first exposure and by the time the dark is taken the dark will overcompensate and produce dark spots. It is almost impossible to have the sensor at the same temperature for both darks and lights.
I have never had any joy out of taking darks before or after a series of exposures and correcting in the computer later. I have tried every possible method even working with all fits files. To this day I have found NOTHING and I mean NOTHING beats ICNR. Canon do something very cunning at the individual sensor pixel level. ICNR also eliminates amp glow.
It doubles the time needed for data collection but at least the data is as free of noise as is possible.
There is nothing wrong with your cameras sensor. These spots are more noticable as summer weather arrives.
Here is a little gif 300k
http://members.optusnet.com.au/~fmlee/mk4.gif
Bert