Hoping there is someone out there that can help with this one.

We are having issues with ROS and WebRTC, its seems to be NAT issues with the ALG/NAT Helpers.

As far as we can tell there is some sort of port mismatch happening during the process.

When testing WebRTC behind another router Cisco/Billion, connections are fine. Its only when Mikrotik NAT comes into play.

Has anyone else seen this problem? I know people have had issues with SIP and disabling the SIP Nat Helper has resloved the issue, however in this case it doesn't help.

There are no ALG's for WebRTC in RouterOS, there are only ALG's for SIP, FTP, TFTP, H323, and IRC. Only IP address and TCP/UDP port translations, due to standard source-NAT'ting, would be occurring with WebRTC. The WebRTC protocol RFC does require ICE, TURN, & STUN implementations in the WebRTC clients to allow the protocol to get through NAT. I've never had any trouble with WebRTC through any of our Mikrotik routers. I would think that there is some other difference in the Cisco vs. Mikrotik configurations that's effecting you. If I were you, I'd capture the WebRTC SDP negotiation as done through the Cisco and then through the Mikrotik and compare and contrast.