If you are using a single dark then that's the problem. It's possible during the acquisition of the dark there was a cosmic ray hit which would cause the loss of real data during the reduction process.
The way of handling darks is to take 10-15 darks and median combine them. The median combine will ensure that odd effects such as cosmic ray hits will not turn up in the combined dark.
Save the combined dark, but be aware that library darks have a limited shelf life. You should prepare a new library dark every 2-3 months.
Regards
Steven
http://users.westconnect.com.au/~sjastro/small