Part Ref Frame misaligns from Cad as soon as I start the program

Part Ref Frame misaligns from Cad as soon as I start the program

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I'm losing my mind here, and believe it's because of a fundamental misunderstanding of how to set up a program and what the machine is thinking during an alignment.
Been lurking on the forum a while and studying up. 

We have a repeated, but not repeatable issue where a handful of parts will run perfectly fine, then reload the program and start over, CAD and Ref frame in sync until the moment play is pressed. 
Translating / Rotating CAD nor Transforming the entire program about its axis create a functioning program.

1st picture is a freshly loaded program.
next is as soon as I press start. Yes, I see it calling out plane 1, flipping that has no positive effect either.

Please help, 
sincerely, man on Gantry Bridge