My Grbl Shield is acting- Strange…

Hi, I have had a retro fitted 5400 Sherline mill that I received from our high school for about a year now. I have poked and prodded it here and there only to find I am stuck here and there on bizarre problems. Lately however I have been very active with this machine and a manual mill and lathe, so yes- I am very much a beginner.
However, over the last day I have solved a number of problems that have been bugging me for ages. My backlash (my biggest issue) has been mostly eliminated, I have eliminated the original 1996 broken parallel port controller and replacing it with a v.9 grbl shield which correctly moves its stepper motors at 48 in/min on all axies, I have learned to use inventor pro (I think) to model a part, then simulate 3-axis milling (Even designed my 4 flute .25 diameter end mill) and have uploaded it successfully to v1.09 universal gcode sender. And after all that work, I have one problem I am completely lost on.
Currently I am trying to mill a 1.7×1.7×1 inch block of wood into a 1.5×1.5x.5 inch block of wood. When I upload this to the grbl shield it activates and seems to act as expected. The machine is started at one corner of the work piece and should move down, then face all four sides of the part by traveling around the part twice. Yet it moves to a bit off toward the center of the part and then plunges, okay maybe that’s my fault. But then I tried doing the exact same process ( without the work piece and vice in the way ) to see what may have happened afterword and found that instead of repeating the previous action- the machine moved one direction then plunged. I do not have limits set so it seems that homing should not be the cause. repeating another time causes the part to again move one direction but this time plunge an inch more that expected.
Can ANYONE explain what i Have done wrong here? I have played with the settings, zeroing axies, etc for several hours and still cannot seem to find an answer that may just be plainly in my face.