It seems that mydns-ng is not in active development for a long time and there are major bugs (like axfr transfers to other dns servers not working). From version 3.0.2.2 Ispconfig support bind again and several of us that have installed Ispconfig from the start (version 3) are stuck with mydns-ng. I'm asking for an proposed procedure to migrate our running ispconfig 3 servers from mydns-ng to bind. I think it is a major issue now, because of the lack of support for mydns-ng and the major issues that it has. So if anyone has a proposition how to change a running system from mydns to bind, i'm eager to here it.
I did this a while ago, please see the post below for more information: http://www.howtoforge.com/forums/showthread.php?t=44069
