I'm using the same board with VLANs on the onboard NIC while I wait for my low-profile Intel to arrive and it's working perfectly for me on 1.2.3 prerelease, so you might want to try upgrading.
Otherwise disabling hardware tagging might be worth a try (ifconfig re0 -vlanhwtag), or just buy a decent NIC (though these are miles ahead of the RTL8139 - I can actually get about 95Mbps throughput on this board).