Dug into the cabinet this morning with my morning coffee. Hopefully this helps:
In order to get the button changes to reflect in CPWizard I needed to exit CPWizard and start it up again. With that said, here are some things that may help:
1. ctrlr file - Yes, I do have one. It is defined in my mame.ini and the folder path is set in CPWizard. I have a seven button layout and it defines the default layout for neogeo versus other arcade games. my ctrlr file is named "default.cfg"
2. cfg files - Ensure the path is set correctly in CPWizard. This is important in order for CPWizard to see the changes.
3. CPWizard needs to be running as an application in conjunction with Mame. If you exported out the CP's you will have to export them out again with the correct config.
Other CPWizard info you may find helpful:
1. CPWizard uses a controls.xml file in the data folder to define which buttons to use, layout, etc. You can edit this to ensure correct button naming, etc.
2. CPWizard also uses the colors.ini to define each button color. You can also edit this.