I agree with your suspicions Vulcan.
If this is the case, then whatever, just don't say so here.
advice, before you go playing with the card, take an image of it, and verify your image is good.
might help to know
which CF Card, and what the controller chip is. For example chips like SM series have tools for writing the firmware, including serial number, Phison have tools such as MPtool and UPtool that does the same thing.
These tools are notoriously tricky to use due to poor translations, poor/no documentation etc. I guess because you are not meant to have them unless you are a device manufacturer..
practice on other cards first, and be VERY sure about what you are doing if this is indeed a protection. Might be easier to RE the software.. It usually is.
http://www.usbdev.ruhttp://flashboot.ru