Z axis at print is lower than when I home
I found the issue. When the hotend and bed are at temps for PLA everything works fine but at temps for ABS the Z offset would get all messed up. After a bunch of testing I was able to track it down to a single gcode statment G1 Z15.0 F6000 
At the higher temps my Z stepper skips steps at that feed rate. 

The "Custom FDM printer" machine settings I used for my printer in Cura had that statement in it and so did the cat gcode that was on the card from the factory. I changed the feed rate to 200 and was able to print in ABS.

I was surprised Marlin didn't have a 'limit the feedrate for Z to this number' setting.