Below is a working config snippet for Q-in-Q config between EX9200 and EX4600. EX4600 and QFX5100 should work with exact same config. Since it looks like your QFX side is right, I'd check the MC-LAG pair, which I am not sure is which product and with what SW version. This is using AE/LAG interfaces running LACP which should also be your case.
VLAN Name was 4550 in it as their network has a mix of EX4550s and EX4600s running Q-in-Q to EX9200 MC-LAG Core. On EX4600 ae1 is uplink to Core, while other AE's connect to the plain Q-Tag switches (EX4200s).
Good luck
Uplink to EAX9200
set interfaces ae0 flexible-vlan-tagging
set interfaces ae0 mtu 9192
set interfaces ae0 encapsulation extended-vlan-bridge
set interfaces ae0 aggregated-ether-options lacp periodic fast
set interfaces ae0 unit 448 vlan-id 448
set interfaces ae0 unit 4010 vlan-id 4010
set interfaces ae0 unit 4020 vlan-id 4020
set interfaces ae0 unit 4050 vlan-id 4050
Uplink to Access Switch
set interfaces ae1 flexible-vlan-tagging
set interfaces ae1 mtu 9192
set interfaces ae1 encapsulation extended-vlan-bridge
set interfaces ae1 aggregated-ether-options lacp active
set interfaces ae1 aggregated-ether-options lacp periodic fast
set interfaces ae1 unit 4020 vlan-id-list 1-4000
set interfaces ae1 unit 4020 vlan-id-list 4094
set interfaces ae1 unit 4020 input-vlan-map push
set interfaces ae1 unit 4020 output-vlan-map pop
set vlans ISD-PVT-4550-Management vlan-id 448
set vlans ISD-PVT-4550-Management interface ae0.448
set vlans ISD-PVT-4550-Management l3-interface irb.448
set vlans TEST vlan-id 200
set vlans service-vlan-BACS interface ae0.4050
set vlans service-vlan-BACS interface ae2.4050
set vlans service-vlan-BACS interface ge-0/0/3.4050
set vlans service-vlan-BACS interface ge-1/0/3.4050
set vlans service-vlan-DMZ interface ae0.4010
set vlans service-vlan-Internal interface ae0.4020
set vlans service-vlan-Internal interface ae1.4020
set vlans service-vlan-Internal interface ae4.4020