The default values for both backgroundColor and expandedBackgroundColor in JuiceboxBuilder-Pro are both '222222'. These values are noted as defaults in the Config Options page.
I've just double-checked this in my own installation. When I click the color box next to 'Background Color' (in the 'Customize -> Lite' section) or 'Expanded Background Color' (in the 'Customize -> General' section), '222222' is displayed as the default value.

Default values are not written into the 'config.xml' file but if you change both of these values to black ('000000' with opacity '1'), then the following values are written to the 'config.xml' file:

expandedBackgroundColor="rgba(0,0,0,1)"
backgroundColor="rgba(0,0,0,1)"

... and the following is also included in the embedding code in the 'index.html' page:

backgroundColor: 'rgba(0,0,0,1)'

If you do not see this behavior, then try uninstalling and reinstalling JuiceboxBuilder-Pro and make sure that you are using the most recent version of JuiceboxBuilder-Pro (v1.4.3) to ensure that any bugs present in previous versions which have since been fixed are not contributing to your problem. You can check which version you are using by going to 'Help -> About JuiceboxBuilder-Pro' from the drop-down menu at the top.
If necessary, instructions for downloading the current version and upgrading JuiceboxBuilder-Pro can be found on the Upgrading Juicebox support page.

If you set a gallery's background to be transparent (by setting its opacity to '0'), then, by default, the background will be white (the default background color of an empty tab/window in a browser) unless you have something else below the gallery the gallery using HTML and CSS.

Please note that if you set the expanedBackgroundColor to be transparent and also set useFullscreenExpand="TRUE", then the actual expanded background color might be white or black depending on the default color that the browser chooses to use when the Fullscreen API is used. (For example, Chrome uses white and Firefox uses black.) For consistency when using useFullscreenExpand="TRUE", I would recommend using an expandedBackgroundColor with an opacity of '1' (fully opaque).

I see the problem you are describing.

Default values are not written to gallery XML files as they should not be not necessary. If a configuration option is not explicitly listed in a gallery XML file, then its default value should be used.

However, the exception to this rule is that if you do not explicitly set an expandedBackgroundColor, Juicebox uses the backgroundColor (for consistency between the normal and fullscreen displays).

The workaround to this would be to ensure that you explicitly set an expandedBackgroundColor.

The only problem with this is that when you use an expandedBackgroundColor with transparency and set useFullscreenExpand="TRUE", the actual background color is dependent on the browser as different browsers use different background colors (black vs white) for the default fullscreen visual environment.

The best course of action to workaround both issues above would be to explicitly set an opaque expandedBackgroundColor.