Hi,
have you got any solution?
As I have on one site (company branch office) exact same problem 
ADSL modem acting as bridge, Mikrotik RouterOS (v2.9.50) managing PPPoE connection. (traffic from LAN is NATed)
Some websites don’t load anytime, some others have big timeouts, But most of websites works fine.
Unfortunately one of “don’t work” website is also “Windows Update” so clients on that site can’t properly update their stations.
I have tried lower MTU/MRU but woth no effect.
There is also VPN (L2TP) tunnel (over ADSL) to other site with Mikrotik (connecting local LAN to LAN on company central) which works fine.
When I specificaly route not working websites over that VPN (so connection to website is over company central) these webs starts working fine.
But this is just workaround, not realy solving problem.
One solution could be route all traffic from branch office through VPN tunel to Central and there to internet, but it would significantly raise bandwith demand on central (costs money) and also it would be waste of payed bandwith on branch office ADSL connection.
So if anyone have solution, please answer.