[xodus matrix modchip bios flash]

From the manual:

The Matrix has 4 user modes and 1 programming mode, the programming mode is
automatically entered when the Matrix is attached to the supplied programming
device. This mode is independent of the dip switches.
It is recommended to set the desired mode whilst in mode 1 (green LED flashing) and
the power to the console on. This will insure that the Matrix remains aligned while you
change mode. The mode change will only take effect on the next power up.
Mode 1 (Dip switch 1 & 2 ON)(LED: Red or Green flashing) Test/Disable
This mode is primarily used for the alignment of the Matrix during installation. It may
also be used to fully disable the Matrix while in circuit.
Mode 2 (Dip switch 1 OFF, 2 ON) (LED: Green) Always On
This mode enables the Matrix to take over the original bios at all times.
Mode 3 (Dip switch 1 ON, 2 OFF) (LED: Green =Matrix, Red =Original) Swap mode
This mode works as follows:
On every power up the Matrix “bios” is loaded indicated by the Green LED. To switch
to the original bios the user must load a game and then press eject, at this time the
LED will turn Red indicating that the original bios is active. To switch back the user
may either turn off and on the console or repeat the above.
Mode 4 (Dip switch 1 OFF & 2 OFF) (LED: Orange flashing) Write enable
In this mode the Matrix is always active but has the ability to be flash updated via
DVD Rom. We do not recommend you leave this mode on permanently, a bad update
of the flash will mean you will have to reprogram the Matrix via the programmer.

 

I don't see why you would need to reprogram the chip.  It is most likely not aligned or not in the right mode.

Matrix_ManualV1.1.pdf