Hi Etherman,
From 15.4, We (EXOS) started supporting CDP protocol and it is enabled by default.
So, the CDP packets may be processed by the switch and not forwarded across to the Cisco device. Try disabling the CDP protocol on the Extreme switch(which were upgraded to 15.4 and above) ports and check if that helps.
Command: disable cdp ports <>
if that does not help, the following article will guide you to configure l2tp profile to allow the CDP packets.
https://gtacknowledge.extremenetworks.com/articles/Solution/Layer-two-layer-2-protocol-packets-does-...
Hope this helps!