True. It sounds like it probably wouldn't be able to load any of the CEL propclasses, which means it probably can't find the CEL directory. Recon: do you have the $CEL environment variable set? I usually put it in my .bashrc file, along with $CRYSTAL.
As far as the Jamfile, that is auto-generated. To have your changes stick, you'd have to modify Jamfile.in. However, I don't really suggest doing that modification, as it could lead to collisions if you try updating from svn. It's much safer to just tell configure where to find mysql.