On EX4400-VC setup, the interface on the back up chassis remains down after a reboot.
In a EX4400-VC setup, if the VC is rebooted, the interfaces on the backup chassis does not come up.
The issue might not be seen on every reboot. But should be recreated after on an average 2-3 reboots.
The issue that interfaces on the Junos are seen as up/down. However in the BCM, it appears as UP. This is because there is auto-negotiation mismatch between BCM and Junos. On Junos is detects as incomplete.
This issue can be recovered by simply bouncing the port.