Appaerently Thunderbird 3 now allows the column headings to be set on a per-folder basis. While this is might be a neat feature, it is also quite a pain for all the others wanting one default column list for all their folders. Luckily, there's a workaround to accomplish this:

Set layout for the uppermost folder ("INBOX")
Quit Thunderbird

Delete all but the INBOX.msf .msf files from your profile directory:

find ~/Library/Thunderbird/Profiles/*/ImapMail -name "*.msf" \
         -a ! -name "INBOX.msf" -exec rm -v '{}' +

Start Thunderbird again, now the default layout should be propagated to all the subfolders.