HD Native PCIe + Symphony I/O + Magma Express Box 3T Issue

[stevepoint]

I have what I imagine is a somewhat unique set-up:

2012 non-Retina Macbook Pro - 2.6ghz Quadcore i7, 16gb RAM, OS 10.8.5
Magma ExpressBox 3T Thunderbolt Chassis
HD Native Card inside Chassis (up to date firmware)
Symphony I/O connected via Digilink to HD Native Card
Pro Tools HD 10.3.6/11.1.1 (problem happened pre-PT 11, and on all earlier versions of PT HD10 and previous OS versions)

Problem:
The Symphony I/O almost always is not recognized as connected to the HD Native card when I boot my system (both when checking Avid Core Audio Manager and within Pro Tools). Whether it does show as connected and how often, is completely random as far as I can tell.

i.e.
- 10% of the time it connects on the first boot up
- 30% on the 2nd try
- the other 60% it can be anywhere from 3 restarts to 10-15 before the HD Native card sees the Symphony IO

I can't reliably tell if resetting the Symphony I/O and/or shutting down the computer vs. restarting it makes a reliable difference as the consistency of this problem is all over the place. I'm never adjusting any cables or settings between the times when the interface does and doesn't connect.

As far as I can tell, all of these components are supported and should work. I even had my Symphony IO replaced (for this reason and a couple of unrelated reasons) and it behaves the same way as the previous unit. I don't think it's a Magma issue as I have a UAD Octo card in the chassis and it always shows up regardless of if the interface connected.

I've had the problem when running the OS in 32-bit and 64-bit.

Any ideas?

Two days ago I booted up and it connected on the first try - yesterday I continually rebooted for 45 minutes before it finally connected - very frustrating. Thanks for any help that anyone has.