This can only happen if your switches are not connected properly. i.e the trunk is not configured properly and the Vlans are not allowed on the trunk. This could also happen if you dont have STP BPDU's propoerly exchaned between the switches.This is moreover related to the configuration of the switch. If you have a proper configuration end-end on your LAN switches, you should not face any problem such as the one mentioned above.
You probably have to go to each switch and check the trunk configurationa nd you have to make sure that all the Vlans are allowed on the trunk ports.
HTH,Please rate if it does.
-amit singh
