I am using a modified version of the Dual Semi program to drive a robot that uses a Vex controller and two 883 IFI PWM controllers to drive a 12v Globe motor robot. the RC works fine on the pwm motors, (I think I am using motor ports 1,2).

I just added another VEX motor on channel 5. While it works fine if I say motor[5] = 127;

When I try using the RC it pulses like it it is a 1/2 second loop.

Is there something different about how channel 5 and 6 are programmed from the RC unit?

I think you accidentally posted in the wrong sub-forum. This one is for FTC (FIRST Tech Challenge) which uses LEGO NXT + Tetrix, not Vex.
Just above this one, under the competition forums, there is one just for Vex related competitions: http://www.robotc.net/forums/viewforum.php?f=53

If you post there, I think you'll get a better answer.
FYI.