it seems that since 3.1 not all backends are being queried anymore. e.g.: using geo backend first and gpgsql backend second the query will stop after finding a CNAME in the geo backend, even though the cname is within the same zone that powerdns is authoritative for.

for details and example config please have a look at this thread: http://mailman.powerdns.com/pipermail/pdns-users/2013-January/009535.html