I've got some major MTU issues that I've been pulling my hair out over for quite some time. Here's my scenario:
My upstream connection's MTU is needs to be set to 1460 (according to my provider's engineers). I have a MT Router set up as a PPPoE client connecting my network to the internet. Behind it, I have a bunch of servers & another MT Router, which is set up as a PPPoE Server for all of my own customers. If I deviate from 1460 on the main internet connection, communication with my servers (web, mail etc.) dies. On the other MT, I am using VLANs to separate segments of my network. I've created bridge interfaces on top of each VLAN & have added a PPPoE Server & hotspot server to each bridge. The problem I am having is that no matter what MTU setting I put on my PPPoE Servers, something always breaks. I've been testing this recently with 2 different websites (because they've been an issue for my customers). One is http://www.newegg.com, the other is http://www.hotmail.com. If I set my MTU to anything below 1460, newegg loads fine, but hotmail chokes. If I set it to 1460 or higher, hotmail starts working, but newegg dies. There are other websites that are affected as well & I've yet to figure out the complete scope of the problem. If anyone has any suggestions on what to try, I'm at my wits end....
BTW: I've changed the MTU of the VLAN interfaces to 1496, to account for VLAN overhead, & that seemed to help with a few of the other websites that were affected, but hotmail & newegg are still giving me problems.

how about 1504 mtu on those physical ethernet interfaces with vlans on them. just a shot in the dark - i had to use 1504 on one of mine for some reason for things to work.