When forwarding Cisco PVST frames, the EX4650 appears to be swapping the C-TAG for an S-TAG instead of pushing the S-TAG.
If you take a packet capture you will see the packets being sent with the S-TAG to the cisco switch. S-VLAN = 4001 C-vlan = 555
To forward the cisco PVST frames correctly, you will need to enable L2PT:
EX3400-1---ge-0/0/0-----ge-0/0/1 EX4650-1 ge-0/0/0 -------- ge-0/0/0 EX4650-2 ---ge-0/0/44------gi0/44 Cisco
EX4650-1
set protocols layer2-control mac-rewrite interface ge-0/0/1 protocol vstp
EX4650-2
set protocols layer2-control mac-rewrite interface ge-0/0/44 protocol vstp
After that change the BPDUs will be sent to the cisco switch with both tags (this behavior is expected)