I think I know what the problem is.
A gallery's 'config.xml' file holds image size information and when you load a gallery, the image size information held in the 'config.xml' file will be used (or gallery default values, rather than custom default values, if image size information is not explicitly specified).
Custom default values will work only if you create a gallery from scratch using JuiceboxBuidler-Pro.
Try saving custom default values and then close and reopen JuiceboxBuilder-Pro and check the image sizes (click 'New Gallery'). You will probably find that they are your own values.
One possible way to workaround this would be to add the image size information to your gallery's 'config.xml' file before you open the gallery in JuiceboxBuilder-Pro.
As you initially create your galleries with the Lightroom plugin, you could add the image size information to all your gallery 'config.xml' files by adding the required configuration options to the template file that the plugin uses to create the XML files.
Open the 'juicebox_pro.lrwebengine/config.xml' file in a plain text editor and add the following on line 34 (currently a blank line just below "<juiceboxbuilder"), changing the values as required.
maxImageWidth="1024"
maxImageHeight="768"
imageQuality="80"
thumbWidth="85"
thumbHeight="85"
thumbQuality="90"
useSmallImages="true"
smallImageWidth="800"
smallImageHeight="600"
smallImageQuality="80"
useLargeImages="true"
largeImageWidth="2048"
largeImageHeight="1536"
largeImageQuality="80"
Each time a new gallery is created with the Lightroom plugin, the image sizes will be in the 'config.xml' file ready for JuiceboxBuilder-Pro.