Hi , I'm writing this for anyone else that might experience this same problem somewhere in the future and the solution for said problem.
*IP/IP or GRE tunnel connected between Mikrotik and Linux Quagga box
*OSPF Configured in Point to Point mode to exchange routing information.
*Correct Firewall rules installed to allow secure communications.
*MTU Values verified to be correct on either side.
*IPIP or GRE tunnel comes up and there is full tcp/ip connectivity.You can ping , ssh , sftp into remote sides a-ok.
*The Mikrotik establishes a 1way/init relationship with the Quagga box as evidenced in the following command on the Quagga box
#sh ip ospf neighbor
X.X.X.X 1 1Way/Init 37.416s X.X.X.X ipiptunnel:X.X.X.1 0 0 0
*The Quagga box does not not form a relationship with the remote side , and your Mikrotik will be neighborless
*Torch shows occasional 224.x communication , but your p2p endpoint does not show up in the src list.
*From pretty much everything that I saw this only seems to affect when it goes Quagga-> Mtk . When importing config and running Quagga - Quagga or Mkt - Mkt full adjacencies were formed.
Wanted to kick my own ass for this , but the solution is remarkably simple.I had pushed this config into a testlab and did some tcpdumping only to find that I was getting ICMP Expiry back immediately right after the peers were sending each other messages.
Setting the TTL=64 field in the centos IPIP tunnel field corrected the problem.You can also manually add it via the command line via the ip tunnel add command using a value for the ttl option.
Hope it helps someone , because I was starting to pull my hair out at some stage.