On a FLINT 2 I have a lot of problems during a PPPoE establishment.
From the logs (that now I lost because a reboot) you can see that the port goes up and down.
Sometimes goes down after a successful PPPoE registration sometimes before.
I'm using the latest 4.6.4 with MTK sdk.
Please share your logs
Please try to fix the interface negotiate rate, probably it related to the compatibility issue between the 2.5Gbps.
ifconfig
//Confirm which one interface is the WAN, say if the eth1 is the WAN and fixed 1000Mbps:
ethtool -s eth1 autoneg off
ethtool -s eth1 speed 1000