Quite unlikely to be faulty hardware (i.e. your MT6000.) I would gravitate towards buggy driver, either the ethernet/MAC or PHY driver did not take care of all possible connection variations. Your ISP's modem likely turn on something in the modem's port (e.g. EEE) and it probably confuses the MT6000 network drivers.
Another quick experiment you can try is if you can get 1000Mbps if you connect your computer/notebook's ethernet port (assuming they are only gigabit ethernet ports) to your MT6000's WAN port. Your computer will not get an IP, but it should report the connected speed. See if your computer reports 1000Mbps or 100Mbps. I would guess your computer will report 1000Mbps.