We used to set up a EoIP tunnel and set the MTU to 1500 as per the wiki. Recently tunnels have been getting around 30 to 40Mbps of TCP throughput and full UDP throughput. As soon as I hit the up carrot on the MTU setting and the tunnel goes back to 1458, I am able to get full speeds. I think this might have been broken with a recent firmware upgrade. Will have to play with them a little. I have noticed on CCR1009,1016, and 4011s. Ones running 6.45.7 and another is running 6.46.6.

We have experienced this issue as well. I've been meaning to experiment to figure out which firmware version broke this

Is the link capable of 1542 byte sized frames?

The link is just using 1500mtu normal layer 3 MTU.