Before I installed my 3/4 MDF waste board, I had no problem creating GCode via Fusion 360 to create good cuts with my Onefinity. Now that I’ve added my waste board, every program I’ve sent to the controller has the z-axis about 1/2" to 3/4" above the stock that I need to cut. I’m running out of sanity here…
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Are you zeroing your work offset from the new wasteboard? How were you setting your work offset before installing the wasteboard?
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I’m zeroing my work from the stock on the new wasteboard. I home the machine first, then place the stock on the wasteboard, and use the probing square to zero XYZ on the front left corner of the stock.
When you probe X Y Z it will reset your Z height to the top of the stock, you should then re probe z with the probe turned upside down on the wasteboard.
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Thank you, Derek! That was the step I was missing! I have finally successfully cut out a hole. 
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I’m just curious if what Derek told you to do if that worked because I don’t quite understand if you’re using the probe and probe x y and z then z should be set automatically to the top of your workpiece. So I don’t know why you would have to reprogram z again.
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Matt - What Derek told me to do worked because it tells the controller where the waste board is, which is also the bottom of the stock piece. Since I was previously taking the Z-axis zero measurement from the top of the stock (in my case, a 1/2 piece of plywood), the Z-axis was always a 1/2 inch higher than I wanted it.