The problem you are all experiencing is very common and happens because the plastic you are screwing you matrix in is to soft and fragile...
I'm no expert and this might not be the best way to do things but here is the best solution I found so far...
Required Hardware :
1) Tork screw drivers (the usual ones ... 20,10)
2) A PC Motherboard brass standoff (The brass bolt thingy that you use to bolt a PC motherboard to the PC casing) (Or, worse case scenario : a small bolt and matching screw)
3) Pliers (or even better, a dremmel tool)
Procedure :
1) Remove your Xbox's motherboard from the casing.
2) With the pliers, remove the plastic nob where you would normally screw your matrix into. Dont cut the little metal arm... You'll need it for ground so just lift it a bit and but it back once you have removed the the plastic nob.
3) If you are using a bolt, you can skip this step.
Remove the MALE part or the brass standoff (Thats where the the dremmel comes in handy... but I've managed with the cutting part of pliers and a little sand paper a couple of times).
4) Hold your xbox's motherboard vertically, put the rest of the brass standoff (or the bolt) on the back side of your motherboard. Align it with the whole your matrix is going to use and screw the matrix in (not to tight... you still need to align it).
5) Here is the tricky part... You need to align the matrix before screw it tightly. I usually do it by keeping the board in its vertical position, plugging the power and the power cable (Yello cable set at the front) back into the board. Then put your matrix into test mode. Powerup you xbox a align the chip. Once aligned, tighten the screw and check that the alignment hasnt changed. This is kind of the quick and dirty way to do this.. but you could eventually find a way to attach the standoff to the casing with some sort of contact glue or even a little solder. If you, you wouldnt need to do all this.
6) Put the board back into place and change your matrix to the desired position.
Hope that helps :-)