It looks like (at least in some cases), the /tmp cleaning part of `bootmisc' script tries (and fails) to execute because / is still mounted read-only. I noticed this when one large partition was being fsck-ed (in direct meaning ;) after the computer went down because of a power outage. The error message I saw said something to the effect that "rm: /tmp/somefile(s): Read-only file system", or some such. /tmp shares the same partition with / on my desktop.
did you update all your scripts in /etc/init.d after merging the new baselayout?
Going to put this to "works for me", as we do not get responce.
Oh, sorry, I thought that I replied... Anyhow, my answer was that I have not yet merged the new baselayout. Maybe I should do that first...