4x4x4 led cube problem

It could be a problem with the darlington pair array, you might have it wired incorrectly, or it could be with your LED pins.

The plane determines which set of LEDS are on, so that may be correct, but you may be sending out more than 1 output.

Im not familiar with (B1000,B0000,B0000,B0000,B0000,B0000,B0000,B0000,B0000,B0000,B0000,B0000,B0000,B0000,B0000,B0000,100) as a form of port manipulation. Normally it is B0000xxxx,Bxxxxxxxx or something simular.

Look at this site.
http://tronixstuff.wordpress.com/2011/10/22/tutorial-arduino-port-manipulation/