@pneumoboy:
Maybe coming in a little late, but I have a similar configuration using VLANs without an issue. Basically each subnet is on its own VLAN. For you:
192.168.1.0/24 VLAN1
192.168.4.0/24 VLAN2
192.168.44.0/24 VLAN3
Each subnet's default gateway resides on the pfSense box. And each VLAN has its own Firewall ruleset, which you can use to control the traffic between the VLANs. So it is possible to let both 4/44 talk to 1, but 4 cannot talk to 44 and 44 cannot talk to 4.
My corp configs use one physical interface for the trunked link (for all the vlans), and one physical interface for management (that is not trunked). No one says you cannot use a trunked link for management, but for sanity (and fat finger mistakes) I keep them separate.
I have this configuration setup, but for me the rules are negated by the "Default deny rule" and any connection to the other VLANs are dropped by the firewall.
Any ideas of what a possible problem is?