Yes I had that pin inverted since you suggested it, here is what I have currently setup for my spindle:
loadrt [KINS]KINEMATICS
loadrt [EMCMOT]EMCMOT servo_period_nsec=[EMCMOT]SERVO_PERIOD num_joints=[KINS]JOINTS
loadrt hostmot2
loadrt hm2_eth board_ip="10.10.10.10" config=" num_encoders=0 num_pwmgens=1 num_stepgens=4 sserial_port_0=0xxxxx"
setp [HMOT](CARD0).watchdog.timeout_ns 5000000
loadrt pid names=pid.x,pid.y,pid.y2,pid.z,pid.s
addf [HMOT](CARD0).read servo-thread
addf motion-command-handler servo-thread
addf motion-controller servo-thread
addf pid.x.do-pid-calcs servo-thread
addf pid.y.do-pid-calcs servo-thread
addf pid.y2.do-pid-calcs servo-thread
addf pid.z.do-pid-calcs servo-thread
addf pid.s.do-pid-calcs servo-thread
addf [HMOT](CARD0).write servo-thread
setp hm2_7i96.0.pwmgen.00.output-type 1
setp hm2_7i96.0.pwmgen.00.scale 18000
#*******************
# SPINDLE
#*******************
#setp pid.s.Pgain [SPINDLE_0]P
#setp pid.s.Igain [SPINDLE_0]I
#setp pid.s.Dgain [SPINDLE_0]D
#setp pid.s.bias [SPINDLE_0]BIAS
#setp pid.s.FF0 [SPINDLE_0]FF0
#setp pid.s.FF1 [SPINDLE_0]FF1
#setp pid.s.FF2 [SPINDLE_0]FF2
#setp pid.s.deadband [SPINDLE_0]DEADBAND
#setp pid.s.maxoutput [SPINDLE_0]MAX_OUTPUT
#setp pid.s.error-previous-target true
setp [HMOT](CARD0).pwmgen.pwm_frequency 10000
setp [HMOT](CARD0).pwmgen.00.scale 18000
setp [HMOT](CARD0).pwmgen.00.output-type 1
setp [HMOT](CARD0).pwmgen.00.out0.invert_output TRUE
#setp hm2_7i96.0.pwmgen.00.scale [SPINDLE_0]MAX_OUTPUT
net spindle_output <= pid.s.output
#net spindle-index-enable <=> pid.s.index-enable
net spindle-enable [HMOT](CARD0).pwmgen.00.enable
net spindle-vel-cmd-rpm => pid.s.command
net spindle-vel-fb-rpm => pid.s.feedback
#net spindle-output <= pid.s.output
#net spindle-speed-out-rpm-abs [HMOT](CARD0).pwmgen.00.value
# ---setup spindle control signals---
net spindle-vel-cmd-rps <= spindle.0.speed-out-rps
net spindle-vel-cmd-rps-abs <= spindle.0.speed-out-rps-abs
net spindle-vel-cmd-rpm <= spindle.0.speed-out
net spindle-vel-cmd-rpm => hm2_7i96.0.pwmgen.00.value
net spindle-on <= spindle.0.on => [HMOT](CARD0).ssr.00.out-00
#net spindle-cw <= spindle.0.forward
#net spindle-ccw <= spindle.0.reverse
#net spindle-brake <= spindle.0.brake
#net spindle-revs => spindle.0.revs
net spindle-at-speed => spindle.0.at-speed
net spindle-vel-fb-rps => spindle.0.speed-in
#net spindle-index-enable <=> spindle.0.index-enable
net spindle-enable => hm2_7i96.0.pwmgen.00.enable
#net spindle-speed-out-rpm-abs hm2_7i96.0.pwmgen.00.value
# ---Setup spindle at speed signals---
#net spindle-enable => [HMOT](CARD0).ssr.00.out-00
sets spindle-at-speed true
Just to be sure, when using step-, I should connect p
my PWM board + and - to the step 5 5v and step-?