Having the same issue on a brand new RB951G-2HnD version 6.33.3, any help?
Ok after many hours browsing and trying I found the problem it was due to TCP MSS packet size as some one in other forum suggested, basically the problem is that when you configure the pppoe to modify the TCP MSS it adds two rules to the mangle section at the firewall, but sometimes this rules are not correct, don't know if this is a bug on Mikrotik or an error from the ISP, so you get a lot of fragmentation from the packages so for some sites when you browse the packages are sent and dropped, and sent and dropped in a loop until the time out error appears, the first step is to set up the pppoe profile->General->Change TCP MSS to default value. then on Mangle tab at Firewall Section create a new rule with:
Out. Interface: your out interface (pppoe-out in my case)
TCP Flags: syn
Action: Change MSS
New TCP MSS: here is the catch, here you define the size of the package if its too high you will have DNS problems and fragmentation, if its too small you will have other problems, in my case setting it to 133 did the trick
At PPP section on the Interface for pppoe the Max MTU was set to 1480, Max MRU to 1400 and MRRU to 1400
hope this helps someone else.