I might suggested that MAC Pause Frames may not be the source of DHCP not working. MAC Pause Frames should only be associated with 10GE ports, so I assume these are related to using 10GE uplink ports to connect to the Cisco, or might you be using 40GE interfaces for this connection? BTW, the pause frames, I assume, are coming from the Cisco - have you asked them why this is happening?
If you set a static IP on a [test] device off of the 1GE ports of the EX3400, can it ping the Cisco IP in the same subnet/vlan? Is the connection to the Cisco a tagged trunk port, or access? Is this new install, or are the EX3400s replacing older other Cisco gear, and if yes, did DHCP function properly prior to replacememt? On EX3400 have you enabled any port level security features?
There are probably 5 other questions I have not asked, . . . Do you have a TAC case opened, or no service contract?