Thoroughly check your HD for another copy of resource.library. It might be that a prog that starts on boot up is using resource.library that's stored in it's location instead of the Libs: one, and if it's an earlier one, that'll be the only one in memory.
If you do find one, make a note of where it is (in a txt file is handy), create a new dir anywhere else on the HD and move the lib into there (along with the txt file if you made one).
Reboot. Hopefully now HDToolbox won't complain about not having V44.
If there is no other resource.library on your HD try copying HDToolbox from the 3.5 CD over the one on your HD, reboot and try that.
I've had no experience with CF Cards, but part of it sounds like a library conflict :-)
