Hah, I just encountered this for a completed though similar reason. I'm still not entirely sure what was going on, but in Azure it seems like their network fabric that underpins VM networking stack were combining TCP packets into larger ones between two VMs.
One of those was tunnelling the traffic elsewhere and was getting packets "from the network" with packet sizes up to 65k despite the MTU of the tunnel being set to 1400. The transmitting host was respecting the MTU. I had to force clamp the MSS to the PMTU in iptables to get things working again.
One of those was tunnelling the traffic elsewhere and was getting packets "from the network" with packet sizes up to 65k despite the MTU of the tunnel being set to 1400. The transmitting host was respecting the MTU. I had to force clamp the MSS to the PMTU in iptables to get things working again.