It is weird indeed.
I had a suspicion that the Axe sounds different on different Axes because of installation errors or something for quite a while now... But I can't confirm it. People say "They can't be different, because it's code", "It's the settings" or "He thinks it's worse because oh his taste" but I am a bit suspicious of those claims.
The thread yek made can help figuring this out, but only if he shared DI's. Then again, unlikely, but how could we be sure his Axe sounds right?
Note: The new firmware has no "Reset all amps" option?...
Speculation is getting out of hand...
I've experienced this "bad firmware install" phenomenon once. In 6 years time. And I installed new firmware hundreds of times, if not more.
It was very obvious from the start that something wasn't right. Everything sounded way "off" and thin.
I tried everything such as resetting the system params, resetting blocks, re-selecting amp types, turning global modeling parameters off and on again, disconnecting the foot controller, etc.
Nothing solved it, except for: re-installing the firmware.
I knew what I was doing when it happened. Except for one thing: I should not have re-installed the firmware and should have called FAS Support. Because there might be a way for FAS to create an image of the Axe-Fx's state, which can help Cliff find the cause.
And that's my suggestion to those to whom it happens: "freeze" the Axe-Fx, and call Support.
Regarding my reference clips: there's no need for DI files, really. It's not necessary to have identical sounds.
Use your guitar with single coils or humbuckers, follow the guidelines in the thread, and if it gets anywhere close to the recorded tones, you're set and you don't have to worry.
In the end: if it's some kind of a bug, it's the easiest bug to work around, because you just have to install the firmware again and it's solved. A matter of minutes really.