Hi,
How does the port configuration look like on the EX4550 in terms of port mode (access/trunk) and VLAN configuration? Does Spanning-Tree block Interfaces/VLANs on the EX4550?
When you set up the Port-Channel on the Cisco side the way you mentioned, the traffic should be carried untagged across the channel. You should keep this in mind, when thinking about the issue.
If you want the traffic to be carried with a VLAN-tag (let's say 999), you should use an SVI on the Cisco switch and change the Port-Channel type to an L2-trunk, that carries the VLAN-ID 999. On the EX4550 and the SRX, you then should also use trunk ports that carry VLAN 999.
Regards, Benjamin