Hi,
...
I just checked by putting a led on another's leads but reversed and unfortunately it appears to be working.
I came across the problem you reported a few times now. I had no idea what could be the reason for this strange effects.
It still doesn't make sense to me that LEDs which are wired the wrong way light up at all, but well ... you proved it!??
I' going tol build a small "Not-working-inverted matrix" over the weekend and see if I can make sense of the whole thing.
You probably solved some "MAX7219 Mysterious Light-Effects" postings, because you are the first one coming up with an explanation for the problem.
Will someone please come up with a better reason why its not working so I dont have to desolder that many LEDs?

If the LEDs are on a PCB, you are probably out of luck. But if you build something like this (which would be the correct wiring for the LEDs) with
wires that run from the matrix to the MAX7219

and you inverted every LED on the matrix, you can swap all the segment- and digit-connections and end up with a correct matrix.
You have to wire :
Dig0 on your matrix to the SegDP-connector of the MAX7219 and SegDP from your matrix to Dig0 on the MAX7219.
Dig1 on your matrix to the SegA-connector of the MAX7219 and SegA from your matrix to Dig1 on the MAX7219.
and so on...
That should do the trick
Eberhard