I just purchased a LMS 3990 mini mil that’s had a CNC conversion done using an ESS board, MX3660 stepper driver, and a LMS 4213 CNC spindle speed controller. The issue I have is that regardless of the Spindle RPM I set in mach 3, my machine is at full speed until I set it below ~15rpm. If I set the RPM between 0-15 the spindle speed changes, almost as is the PWM signal is off by a factor 100 or 200. Any ideas?

What are your M3 config settings on the PWM output?  I can't see any recommendations in the 4213 instructions.

Have you set the min and max values in the spindle pulley section and selected pulley 1

Sorry for the late response everyone. I have attached screenshots of my settings. Yesterday I measured the voltage coming from the Leadshine to the mill, when I set the RPM to 3 in Mach3 the signal voltage was about 1v, 15rpm was 6v, 20rpm was 8v, and 25rpm was 10v. Any RPM I set between 25-2500 was still reading 10v. Very weird, definitely some variable a couple decimal places off somewhere.

Your pwm base frequency is very low at 5hz.  Try increasing it to 100.

Have you set your pulley speeds