Parallels has "improved" their support-policy. Now you need support contract or pre-purchased incidents just to report a bug. Because my issue is not on my own box (where I have support), but on a customer's server, there is nobody left for me to complain about this. So, here goes:
For some reason on Parallels Plesk Panel 11.5.30 Update #30 (which is the latest version at the time of writing this) a single and every time the same domain creates a DNS-zone into /etc/bind.conf. That would be fully understandable, if that particular domain would have the DNS enabled. It doesn't. The web-GUI clearly indicates the DNS-service for the domain as switched off.
I did investigate this and found that couple of commands will temporarily fix the issue:
The first command will hit the DNS with a big hammer to make sure it is turned off. The second command will polish the leftovers from the /etc/bind.conf and properly notify BIND about configuration change. The problem is, that the zone will keep popping back. I don't know what exactly makes it re-appear, but it has done so couple of times for me. That is really, really annoying.
Parallels: You're welcome. Fix this for the next release, ok?
Rest of you: Hopefully this helps. I had a nice while debugging really misguided DNS-queries just to figure out a zone has DNS enabled.