My understanding of vtp domains is that a group of switches learns from the switch setup as "server" and gets a list of valid vlans. It then uses normal rules of spanning tree to choose a switch to be used as the root based upon mac address, priority etc (normal bridge priority is 32768 by default). If you have a vlan that is not a valid vlan for a particular vtp domain ie because maybe it doesn't exist then it will not be able to forward the vlan across the switches to another point. You need to add the vlan to the list of other vtp domains to ensure it gets acted upon with normal spanning tree rules.
As for all switches picking the same root switch this is probably a switch with either a lower priority than 32768 eg 8192 and it should be a core switch.
Another possibility for type-inconsistent is that the native vlan's do not match but that may be wrong
