Ok, So I guess i should have added the fact that it is installed per Mimosa Specs to the first post! Because the Troubleshooting Guide basically tells you how to install it properly.
It also states to add a switch in the loop as we have already done, I hope this is not the Answer.
My current choices to make it work is lock it at 100Mbps or use a switch in the loop to get 1000Mbps.
We have connected just about every other brand of equipment to Mikrotik equipment and never had an issue with port flapping thus I am looking at Mimosa as the issue here.
So what is the next move?