Hi Jeffrey

What Peter said ( mux rate of 100Hz ) is true. I always work with that rate.
Perhaps working at so high mux rate you can do the different intensities by soft.
Just an idea
Suppose you work at 400Hz so you refresh the matrix 4 time faster than using 100Hz, then if you have 4 image in RAM of the matrix you can refersh each time with a different image. If a led is refresh with a 1 (on state) the 4 times you have full intensity and with 0 ( off state ) then is off. Of course you have 16 possible levels.
Perhaps you can try this ( leaving your 2 bits of intensity on ) and feedback us.

Good Luck
Daniel