Hi Matt
The checkbox is an image cb_unchecked.gif and cb_unchecked_over.gif, so that why you cannot only change the css to change the background colour, if you need to update all uncheck box with another colour, you can download the image and replace the original after changed colour, the image is under the folder maximouiweb\webmodule\webclient\images before build and deploy.
For test and development, you can direct update the image under maximouiweb.war\webclient\images which is the folder after deployment
Regards,
Jason