Loose VLAN on upgrade to MR6 P1

[#1]

I upgraded my FGT 500A from MR4 P5 and all seemed to be fine except that traffic from one VLAN (vlan1) on a port with several VLANs just stopped. The other VLANs are not being used at the moment. I reverted back to MR4 and all started working again. I then ran the upgrade again and the traffic stopped on the same VLAN(vlan1). Strangely this time the traffic switched to coming out of one of the other VLAN (vlan2). I then reverted back to MR4 and all started working as usual (as it had done for over a year). I upgraded again with the same result - the traffic switched to the other VLAN(vlan2). I then downed the VLAN (vlan1). Traffic then stopped coming from vlan2. As soon as I started vlan1, traffic started flowing again(from vlan2). Traffic is being monitored by snmp using PRTG. I am confused as I am sure you are - any ideas?????