I built a 5x5x5 blue led cube. The problem you are having is that the brightness will vary based on the duty cycle of your scanning, and the number of led being commanded on at any one of the five levels. You really should have a dedicated resistor wire to all 125 leds, that would eliminated the variation of brightness due to the number of led selected on for each level.
The solution I used, which is the best was to use shift registers that had constant current regulators on each of the output pins that would automatically adjust the output current to whatever value you wanted via a single 'current programming' resistor wired to the shift register.
Here is a link to a cube project that I used for controlling the cube, but of course I used an arduino standalone chip to drive the thing rather then a PIC micro that this project uses. Anyway the constant current drivers work great and allow scanning without any resistors in the cathode or anode circuits of the LED. The arduino turns on each row in turn for 2 milliseconds via a transistor wired to +5vdc, while the 25 bit outputs a active low constant current output shift register turns on one vertical row of 5 levels of leds. Works great, very even brightness no matter what the pattern being displayed is.
Lefty