I tried to repeat this bug in the current unstable package (20090814) and I cannot. My custom certificate I added to /usr/local/share/ca-certificates was added to the proper directory and retained after running dpkg-reconfigure ca-certificates.
Cheers! Lee Azzarello -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org