Max CL will configure the outputs to certain pins and you cant assign them to anything else no matter what you put in Ports and Pins.
Pins 2 to 9 are quadrature outputs for axis A to Z, ie 2 and 3 are quad outputs for A, 4 and 5 for Y , 6 and 7 for X and 8 and 9 for Z
It would seem that if you are getting motion from your drives on some of these pins with Max CL enabled then your drives are using Quadrature input rather than Step/Dir.
I would suggest you see how to set your drives as Step/Dir and then disable Max CL mode and that way you will be able to configure things in Ports and Pins as you wish.
You will find the Pinouts for Max CL mode here
ftp://anonymous@machsupport.com/ExtraInformation/MaxCLPINASSCL.TXTHood