I'm glad to hear that you have been able to resolve your problem.
Thank you for letting me know.
Here are a few notes which might help with a few other things...
It seems the images have to be in the same level directory as Juicebox.
If you create a gallery with JuiceboxBuilder-Pro, the application uses the default gallery structure and saves the images to a folder named 'images' directly inside the gallery folder.
The web page containing the gallery's embedding code should also be directly inside the gallery folder (for example, the 'index.html' file generated by JuiceboxBuilder-Pro).
You can change the location of the images if you like but you'd also need to manually change the paths to the images and thumbnails (the imageURL and thumbURL entries) in the gallery's 'config.xml' file (so that Juicebox knows where they are).
The imageURL and thumbURL entries can be either absolute paths (staring with http:// or https://) or relative paths (relative to the web page containing the gallery's embedding code).
If you want to move the entire gallery folder away from the web page containing the embedding code, you can use a baseURL in the embedding code to point towards the gallery folder.
In doing so, you can have the gallery folder anywhere on your web server (with no need to modify any paths in the gallery's 'config.xml' file).
Instructions for using a baseUrl can be found here.
For the record, the software cannot process more than 150 or so images at a time, or it crashes, losing anything processed since the last save - so it's necessary to save often for large galleries.
There is no limit to the number of images that you can have in a gallery but, as you have discovered, you might not be able to add all the images to JuiceboxBuilder-Pro at once.
Unfortunately, if you try to add many images to JuiceboxBuilder-Pro at once, then Adobe AIR (the platform on which JuiceboxBuilder-Pro runs) may not be able to allocate enough memory for the task at hand. Even if your computer has plenty of free RAM, Adobe AIR applications are limited to around 1GB of memory allocation (as far as I can recall).
The workaround (as you are aware) is to add your images in multiple smaller batches. Trial and error will help to determine a safe number of images per batch (it will depend on your own images). From your notes, it sounds like you should be able to add images in batches of 150 (or fewer).
I hope that adding your images in a few separate actions instead of just one is not too much of an inconvenience although I realise that it is not ideal.
Lastly, it would be nice to be able to return to the gallery upload page after saving, since large numbers of images have to be done in batches.
You should be able to go back to the image upload page after saving a gallery (or after opening an existing gallery). Just click the 'Images' tab (between 'Start' and 'Customize') and you can add more images to a gallery (which you can then re-save on the 'Publish' tab).
Otherwise, try going to 'Images -> Add...' (Ctrl+A) from the drop-down menu at the top.
I hope these notes help to clarify a few things.