So I'm about 90% certain that this is a slicing problem.
If I'm in the web interface and send a g28, everything is perfect. Goes right to the front left corner drops until Z triggers. If I follow that up with a g29, it proceeds to probe the entire bed, no issues there.
Now, if I pull up simplify3d and slice a model (In this case a 20x20mm cube, it homes X and Y and starts dropping the Z without moving first to the tool offset of x45,y15 so it attempts to drop into empty space.
So I attempted to see if the g29 would happen after that point by artificially triggering the Z probe (Holding a metal ruler under it flat against the bed but sticking out enough to trigger the probe) the probe stops at that level, rolls over to the first probe point, then throws a "Error: Z probe was not triggered during probing move" and attempts to just shoot over and start printing willy nilly.
This has to be a slicer issue right? I mean sending the codes manually in sequence acts exactly like it's supposed to.
This happens both in Slic3r and Simplify3d.