I posted about this issue with my STT camera (or it appears to be the same issue) about a month or so ago. It happens on short exposure, calibration frames in my case. I interpreted it, perhaps incorrectly, not as skipping and duplicating frames as much as misnaming some of them... Possibly because something wasn't shaking hands properly or not keeping up. Either way, the correct number of frames shows up, but they are incorrectly named - as you describe.
In my case, though, occasionally, SGP will eventually tangled up and crash. I was able to duplicate the problem on two different Windows 7 Pro laptops, both on my telescope and with nothing connected to the laptops but the SBIG camera.
It only seems to happen on very short duration exposures, and putting a delay between exposures will sometimes, but not absolutely always, help.
Jarod had taken a quick look at this, and the next task was mine... To install the new SBIG driver which lists "improved low-level USB communications" as one of its features. Alas, I haven't had a chance to get to that and report back... It doesn't seem to be a widespread problem, but it is repeatable for me.
Are you seeing this with all the latest and greatest SBIG drivers and firmware?
Best regards,
Craig Smith