Yea, It's gonna make me replay the whole section.  I'm now at clue 10 of 7.  I also just noticed that its not rewarding me with Fate or Glory for these. Despite I've played almost the whole game (including these missions) on hard +50 or more.

I'm now playing the Inquisitorial Fortress mission.  Which I believe puts me again back just after the walker mission?

Yes, after several attempts it let me move past that cut scene transition.  However now I have an even more infuriating mission.  At first I thought you guys had even lazier re-usage of missions than the pre-launch debugging.  But then I realized I was actually just replaying the entire Through Fire and Flames missions.  And not always in order.  I've now had to do the buggy tank mission twice, I've now cleared and rescued the guy that lets you later pilot the walker ( I assume based on how it handles it's a low end warhound titan?)  Which pilots pretty crappy based on it getting stuck on literally every piece of terrain if you don't stick to the the roads.

so recap of the order:

played through all of fire and flames.

-> played the walker mission

-> Clue tracker is now at 8 out of 7  though it was just a text glitch

-> then the tank mission again

-> then re-played rescuing the guy with the walker

I assume once I'm done replaying this mission. I"ll have to replay the walker one yet again.  Which, let me be clear as crappy as the walker pilots, it actually feels powerful and almost fun to play it, where as the tank is slower in every possible way than my regular on foot melee build.  Movement, killing, tracking targets.  All of it just feels bad.  It's like being punished for having been effective at playing the game the whole way through to this point.  I'm sure for some people who are less used to hack and slash style games they've been getting worked over so the tank felt great.  For at least me, I felt like I was being held back by the thing.