I'm not sure if you have the same scenario as I do but let's try.
I assume you have private subnets on both ends? Let's say Cisco site has 192.168.10.0/24 and MikroTik site has 192.168.20.0/24. Then you need to exempt your subnets from NAT so it goes through. It was something I had to add to the MikroTik config, it didn't do it automatically.
To do this I went (in WinBox) in to IP - Firewall. And on the NAT tab I added one srcnat rule. In the General tab of the rule, the chain is srcnat, Src Address is MikroTik's site subnet, 192.168.20.0/24, Dst Address is the Cisco site subnet, 192.168.10.0/24 and on Action tab it's Accept. Then you have to drag that rule to the top so it's before the masquerade rule.
Of course the Cisco has to be set up similiar, i.e. NoNat on the same traffic.
Hope this helps.