Scooby-Doo, you should really get your facts straight before answering a question. In a version 1.1 XBOX, a Matrix modchip will flash red continuously IF the modchip isn't aligned properly.
If there is a proper alignment, the Matrix will flash green for a second and than it will flash red. This, however, doesn't put one into the clear. If you change the Matrix to mode 2, 3, or 4, and you get the unbearable on-off, on-off, on-off, this means that you really didn't have a proper alignment.
The easiest fix for this (depending on how you look at it), will be to take out the motherboard, solder a wire to the alternate d0 site, and take the other end and solder it to the top of the Matrix d0 pogo pin. It may sound difficult, but it's actually quite easy to do. Remember to put a piece of electrical tape over the original d0 point, so there isn't any contact between the pogo pin and the motherboard. The LPC points should still be making contact with the pogo pins on the Matrix.
Hope this helps