I noticed the OwnDDNS v. 0.0.2, the update does not work with BIND9 DNS. I just also played with TTL but without success. OwnDDNS update of the client works but the BIND9 DNS is not updated.
In OwnDDNS version 0.0.1 it works perfectly and quickly.
Use i-MSCP Version 1.1.11
Ubuntu 12:04 x64