If you could share some more info on your deployment, like used endpoints, how everything is set up,
version numbers, how much bandwidth is available, how much is allocated, how the call and traffic flow looks like, ...
If its a local=non traversal call then the media should stay within that site.
If it goes out to an other location it will most likely use the WAN.
You could look at the call status and do debugging on the endpoints, incl packet captures.
On the captures you could compare what do you send out and what do you get in and then
talk to the WAN admin again if its not the same ;-)
Depending on your WAN, also check the MTU, so even if the packet is not lost if its not complete
it also causes the same symptoms.
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