RCM4400W pwm problems.

I am trying to use the following port pins for PWM output on an RCM4400W module

PWM 0 : PC4
PWM 1 : PC5
PWM 2 : PE6
PWM 3 : PE7

PWM outputs appear for channels 0, 1 and 3 but PWM2 on PE6 is just noise.
After reviewing the schematics and documentation for the RCM4400W I can see that PE6 does not come out to the connector (JP1 pin 38) unless jumper 1 has pins 1 - 2 connected together.

The problem is that this will also connect the signal CS_FPGA (chip select for the FPGA) to JP1 pin 38 as well.

Does anyone know if driving a PWM output on PE6 will adversely affect the FPGA by driving it’s chipselect line up and down ?