Do you actually have data on that or are you conjecturing? Because I would really love to see data about that if it exists somewhere.
The key thing is each IP 5-tuple (peerA, peerB, protocol, portA, portB) will always take the same path over their network (most likely a different path for return packets, when A and B are switched), so in order to properly probe, you need to probe on a lot of of port combos, and once you find a broken combo, you need to run MTR on those ports, so you can give them the MTR that shows the issue.
Or, if you can, have your internode protocol run on multiple connections and drop connections that are showing issues, and let a different customer file the tickets :)
(email is in my profile if you want to discuss)