Thanks Daniel, now that I know how this works the comments and instructions in menu.lst make more sense. In order to get it to work properly I had to edit the kopt line as you suggested to have the correct UUID for my sda6 but also there is another line # groot=(hd0,X) which I had to set correctly.
Once you've edited these configuration comments in grub.conf, there shouldn't be any more problems - debian and ubuntu don't actually edit that file in any way other than what update-grub does, which is to read the configuration comments and generate a grub config section for every kernel it can find.Also next time there is a kernel update I will know what to check for prior to shutting down or rebooting.