I just installed Multi-Edit 2008 onto my Vista Ultimate 64 system and BCDiffer is working fine there. The BCDiffer.dll file should be located in the main Multi-Edit directory and is loaded directly by Multi-Edit thus no registry access is needed. I have no idea why it wouldn’t work.
One thing to try is to rename your current Multi-Edit directory and then reinstall Multi-Edit and see if that works. If it does then you can copy your changes over to the working directory. If you have changed system macros I’d recommend that you store them in a different directory than the main Src directory. You can compile macros from any directory.