Layer spacing suddenly increasing

For some reason my printer starts moving up higher for each layer than it should be around the time that it needs to retract more. As you can see in the images it prints the bases just fine but then as soon as it needs to do a lot of retractions (which it also does a 1mm z-lift for) it starts raising too much. It seems like it isn't lowering itself as much as it should when it does the z-lift. I'm 100% sure the motors aren't skipping steps, but aside from that I can't understand why this would be happening.

If the motors don't loose steps it would mean the axis is not moving down again.
Either you have to confirm it is really moving up AND down during the retractions or don't lift during retractions.

It looks like you are correct, the axis wasn't moving down all the way. I just did a print with no z-lift and it came out perfect. Do you have any idea why it might be doing that?

Check the gcode for the downward moves. Also the Z rods might be binding. Or the Z downward speed might be too high (or Z driver voltage too low) to make the motor move in that direction.

I'll check out the gcode tonight. Is there a specific setting in Marlin/Slic3r for the Z downward speed?

Marlin has some MAX setting for X,Y,Z,E but I forget the exact names