Hi I'm Jeff Haynes from MVM Tier 3 Support. Have you been helped with this issue yet? If not please send me a PM with your contact information and SR number and I'll make sure we get you on the right path.
I recently went from 6.5 to 6.8 (will go to 7.0 in a few days), also had to upgrade SQL 2000 to 2005 SP2. From reading the Release Notes I believe your problem is that 6.x does not support 2008 (SQL, maybe not even Windows either). I can confirm for you that you don't need to go to 6.7 first; I successfully jumped straight to 6.8 from 6.5. 7.0 Install Guide even said that you could go straight from 6.5 but I heard from multiple techs that probably won't work.
You'll probably want to upgrade from SQL 2000 to 2005 SP2, then from 6.5 to 6.8, then to 7.0, then to SQL 2008 / Windows 2008. As was suggested above I'd definitely recommend opening a ticket and talking to tech support first, that's what I did. Read the Release Notes / Install Guide for each version too, that also helped for me.
Thanks Glitch, your answer is spot on.
Also for anyone who may read this later on down the road, when you upgrade from version 6.5 to 6.7 or later. The way licensing works changes to one centralized component (API Server), as opposed to having to register every device. You will have to renew your license from the server runing the API Component immediately after upgrading, or your scan engines will have problems discovering hosts, etc.
Thanks Talon, actually you reminded me about one mistake I did make:
When upgrading beyond 6.5 make sure that you check the box to install the API service when asked. I misintrepreted this and assumed that the API Service was optional (the kind of API used to hook into 3rd party apps) and I didn't need it since it wasn't installed already, but this is a new service with 6.7/6.8 and is required in order for Foundstone to work. Cost me an extra reboot and about 30 minutes of my time to figure that one out.