Did you do this?
http://forum.mikrotik.com/t/mtu-problems/12811/18
MT is not that great for a PPPoE router. I was hoping to use some of them for certain customers but it’s just not reliable. Those mangles rules work in my office but if I take the same router to a customer site it doesn’t work so I just stopped trying. Hopefully one day MT will make them auto like every other router out there so we don’t need mangle rules or anything like that, just plug and play.