I have been having this problem wince i first started using tomato on my rt-n16. (Shibby Tomato Firmware 1.28.0000 MIPSR2-097 K26 USB Mega-VPN)
Basically certain webpages fail to load, and some will load after refreshing a few times. This affects every machine on the network.
I have tried changing the dns servers to google, and opendns and neither affected the problem.
I have also tried lowering the mtu to no avail.
Is there anything else I can try?