If you're getting the initial openembedded monotone dabase from us (which you are, if you're using our Makefile-openembedded), you're now getting an initial monotone 0.31 database. In order to use this, please also use monotone 0.31.
(Yes, there are newer monotone versions out there. You might have to "mtn db migrate" or something, for details, read http://monotone.ca/NEWS .)
Hopefully, at some point, the database format will become stable. Until, we have this "minor annoyance". Sorry.