VTP (again)

It may seem obvious but VTP only works between devices that are using VTP. What this means is that if you have a trunk port pointing to a router which isn't doing VTP then VTP pruning is not going to work on that link. What's more if a switch has one interface that isn't doing VTP pruning then it means that switch will want ALL VLANs to come over its trunks towards the rest of the network.

The moral of the story - either manually configure which VLANs to forward on the trunk towards your routers OR enable VTP on the router, use VLAN interfaces and put the physical interface in switching mode.