I had a similar problem back along when making an LED sign, all my rows / columns were driven by shift registers, connected to transistors for the high sink / source, the end controller was a PIC micro, this had 1 hardware PWM built in, however, it only drives 5v max and the LED's were driven from 12v, so with my shift register output and a 5v PWM output i used a simple and gate to drive the PWM with great success from the 2 outputs.
Hope this helps? Took me ages to figure out that the AND gate would solve all my problems.