Sounds like you've seen some of the sames things that we have (and learned things that aren't in the System Planner <G>).
The latest firmware does indeed work with non-hairpinning (non-NAT loopback) routers. Our LCP system is working fine with several different brands/models of routers and I don't think any of them can 'hairpin'.
I've also seen the problem with port numbering changing. In fact, we had this problem with an IPSC system recently. Some routers are terrible for this. On an IPSC system, our c-Bridge will also show the port numbers that are in the peer tables for each repeater. I've even seen cases where the port numbers shown in the CPS IP Remote Programming did not match the port numbers as reported in the c-Bridge. That system was really messed up at that point.
I've been trying out the Mikrotik routers, lately. So far, they're working 100% perfectly on our LCP system. I'm going to put them on a 5-site IPSC system, too, and see how they do.
John Rayfield, Jr. CETma
W0PM
Rayfield Communications