Hello,
First things first - there appears to be an error on Your diagram : Your CSCO 6509 Juniper-facing port shows on Your diagram as Gi1/37 but in the printouts it is referred to as Gi1/48.
Secondly, the behaviour You described is expected with inter-switch access ports. In more detail:
1/ an untagged Ethernet frame from Server_04/_03 enters CSCO 6509
2/ it exits as untagged from CSCO 6509 Gi1/48
3/ JNPR EX4200 receives this frame as untagged on ge-0/0/38 access port
4/ JNPR EX4200 passes this frame as untagged to access ports connected to Server_01/_02.
The same happens in reverse direction as well.
HTH
Thx
Alex