******EDIT: I tried adding R1 and it works now. I thought I had tried that parameter before but apparently had not. Thanks for the help!
There was no R in the M569. I tried adding R0 but it didn't do anything. I also tried R1 and R-1 as well as adding M18 as I saw in a similar thread, but to no avail.
Here's the drives section of the setup gcode. The problem stepper is the Y axis assigned to drive 5. I really appreciate the help.
M569 P0 S0 ; Drive 0 goes backwards
M569 P1 S1 ; Drive 1 goes forwards
M569 P2 S1 ; Drive 2 goes forwards
M569 P3 S1 ; Drive 3 goes forwards
M569 P4 S1 ; Drive 4 goes forwards
M569 P5 S1 T3 ; Drive 5 goes forwards
M584 X0 Y5 Z2 E3:4:1 ; Apply custom drive mapping
M350 X16 Y16 Z16 I0 ; Configure microstepping without interpolation
M350 E16:16:16 I1 ; Configure microstepping with interpolation
M92 X80 Y80 Z1886 E420:420:420 ; Set steps per mm
M566 X900 Y900 Z12 E120:120:120 ; Set maximum instantaneous speed changes (mm/min)
M203 X6000 Y6000 Z180 E1200:1200:1200 ; Set maximum speeds (mm/min)
M201 X500 Y20 Z250 E250:250:250 ; Set accelerations (mm/s^2)
M906 X800 Y800 Z800 E800:800:800 I30 ; Set motor currents (mA) and motor idle factor in per cent
M84 S30 ; Set idle timeout