In my Ubuntu server I have a pppoe connection and a lan network.
I have twoo nics eth0 and eth1(for lan) and ppp0<->eth0.

I setup the connection with pppoeconf...and for a few day there was no problem.
After a reboot I had some timeouts with some sites...when those sites wore accessed from lan from a browser. But I could ping some of them.

Then I used poff dsl-provider and then pon dsl-provider...and then the problem disappeared(no weird logs until now). So I rebooted to test...and problem appeard again.

Today I noticed another weird problem... I can not ping linuxquestions.org

I did some google search, I setup some values for mtu on ppp0 like:
1492, 1488, 1460, 1452, 1412, 1400, 1300;

Nothing worked!!

This might be more an issue with your provider based on what you've posted. Maybe a DNS issue. You might need to specify am alternative name server. If you can ping by IP address, but not by name then this could well be the issue here...
If you want to share your current name server config, do
I wouldn't mess around with MTU unless you have an understanding of what you're doing, and what your provider uses. It's unlikely that it was the cause of the initial problem in any case.