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I've run into this issue in a cpl of versions. I have two 48y switches with an AE ESI LAG uplink to a pair of Cisco NX-OS switches running VPC back to me. In multiple versions of Junos, traffic ceases traversing the AE unless I turn off one side of the Junos AE. It is important to note, that the LAG still shows collecting and distributing when traffic is not flowing.
If I turn off AE1 or just AE1's physical ports on switch A but leave it up on switch B, traffic starts flowing. You can do this on either side with the same result. Also, I have the same AE setups running to Proxies, Servers, storage, and other juniper switches, with no issues. Only the Cisco's have issue.
I have a case opened on this but its been hard to troubleshoot. I'm just looking to see if anyone else has seen this and if you resolved it.