Using a Cisco fiber module should work with tagged VLANs. On the combo ports you cannot use a fiber module and copper at the same time. The only other thing I can think of is you have not under VLAN management in the menus added the tagged ports under PORT VLAN Membership to the trunked ports so they support all your VLANs. If you look at PORT VLAN Membership under the menu system you see on ports 49-51 trunk 1UP, 2T, 3T, 4T etc. for what ever your VLANs are as I don't know your VLANs but you get the picture. I am sure this is your problem otherwise it should work fine.