I have the same issue and it appears the errors are mostly annoying rather than harmful.
I also have two separate iSCSI VLANs that aren't routed. I have a single vDS and do port binding according to the best practices -- essentially what you have described.
vmk1 is on VLAN1 and vmk2 is on VLAN2. The EMC VNX array has ports a4 and b4 on VLAN1 and a5 and b5 on VLAN2. When ESXi 5.1 boots up, the host attempts to connect to all array ports via both VLANs. Which means obviously that the connections to a5 and b5 on VLAN1 via vmk1 fail and a4 and b4 on VLAN2 via vmk2 fail.
Is this just a stupid error?