[Dovecot] inbox problems when moving from server to server

this is probably an FAQ but I moved all the mailboxes from a gentoo server to an ubuntu one and all old inbox messages "disappeared" for. New messages appear and can be read, deleted etc. the old messages can still be found in the Maildir/cur directory like they were on the old mail server. Ownership was changed to user:user and is 600 permissions.

Dovecot version: 0.99.14-1ubuntu1

all other mailboxes are fine, all messages visible as far as we can tell.

ideas?