I wish I could of come up with less of a dumb question for a topic subject

I'm having a fairly bad issue I was hoping someone may be able to help me with.
I ordered my control panel through mameroom. I designed my panel through their designer program, then a helpful member here on the boards helped me line everything up. I sent it over and received my panel.
Im at a stage now where Im paying someone to make a custom CPO for me. I went and tried to verify the measurements compared to the file I submitted to Mameroom (that went by the inch, and seemed very accurate). And it appears nothing is exactly as it shows on the program.
For example, the left most edge of the hole for the player 1 joystick
Shows on the designer program as roughly 2 1/4 inches from the left edge
and
On the panel, actually measures to almost 3 3/4 inches.
Is there something I'm not accounting for? or something I don't know that may explain why this is off? and im fairly sure im measuring to the hole on the designer program, rather than the button.
And finally, If I were to try to show accurate measurements for the CPO designer, any chance there is a tutorial out there or could someone point me in the right direction of atleast the program I should be learning to do so ?
Thank you for any help.