Disabling the modchip and then flashing the tsop worked fine with Enigmah since it didn't replace the tsop, it "just" patched selected pieces of the bios in real-time. So when it was disabled you still had the same tsop active (the original one) and could flash it.
Matrix, on the other hand, is an LPC-modchip which disables the original tsop (grounding the d0-line) thereby tricking the xbox to try using the LPC-interface instead (which is probably there for debug-reasons since it clearly says so on the xb motherboard) and if found; the bios will be read from this chip instead.
So; what happens when an LPC-modchip, like Matrix, is disabled after booting EvolutionX with flashing in mind...? Well; nothing...neighter the LPC-chip, nor the original tsop can be accessed causing the "Erasing..."-screen to hang...
At least that is what used to happen before some clever guys designed the evox_matrix-tsop-flash-bios which, by software, enables access to the tsop when the d0-line goes back to normal (thereby disabling the lpc-mod).
What seems to be the problem is that the same clever guys hasn't released a new version of their nice bios so that it can work on v1.1 boxes and that is what me, and presumably a few other guys, are patiently waiting for...