macbook showing wrong keyboard map

My General info:
Running whatpulse (username mep) version 2.0.4 on a Macbook Pro OS X, ver. 10.7.5, Lion. Yes, I’m logged into the only account on the computer. Other programs running are Firefox, iTunes, Word, Stickies, f.lux. Just barely started using this and could not find an appropriate thread using various search terms.

I noticed that the keyboard heatmap is not accurate to my computer. I think this is a really neat idea, taking statistics, but I feel like mine will be very off since I use the “command” button VERY OFTEN due to new tab opening.
Is there a way to toggle this?
Is there anything else I should do since I am running in OS X?

Thank you

The keyboard image is currently a static filled image, so there are no ‘hidden’ keys or something. Also azerty keymaps simply do not show.