I think your menu.lst problem is neither Debian nor Ubuntu, but a change in management of that file by grub itself. Starting from grub 2.0 /boot/grub/menu.lst gets created from scratch on every update of grup, kernel or init.rd, using the parameters given in /etc/grub.d/ (in Debian). If you want to dual boot to another os, you have to place your commands there, and they'll find their way into menu.lst automatically on every kernel update.

That bit me, too, btw :)