Using the version of pdns_server on Debian Jessie, which is apparently 3.4.1, I get the following problem. Given this query:
$ dig @localhost -p 10053 skybo.at -t SOA
With a python bottle.py backend liberally pilfered and bodged from http://jpmens.net/2015/11/03/powerdns-with-the-remote-back-end-and-dnssec/, I capture this with tcpdump: