When using the Machine Control Panel, I've noticed that the Position Readout is wrong after I deploy/retract my Z-Probe.
Normally, after homing my stepper motors, I'm able to use the Jog Controls to move the print-head around and the Position Readout properly displays the position of the head.
However, when I deploy my Z-probe (on a delta with Marlin firmware), it sometimes needs to move the head up so that the probe doesn't crash into the bed. The printer does this without Simplify3D being aware (so it doesn't update the Position Readout), so the readout is wrong (until I re-home the steppers... which is a pain, because I have to move the head back down to where I had it).
It sure would be nice if Simplify3D could notice when I send deploy/retract Z-probe G codes and, when I do, have it re-query the printer for its X,Y,Z position.