1. The nav buttons are "scrambled" that is they just show gibberish instead of the arrows.
Juicebox uses a custom font for the icons in a gallery. It sounds like your web page may be setting a font-family for all elements on your web page using a global CSS selector, such as:
* { font-family: Courier; }
If this is the case, Juicebox will have no option but to inherit such a CSS rule. The font-family will apply to all elements on your web page, including those within your gallery.
Try setting the font-family to the 'body' element of your web page instead (or better still, to only those elements on your web page which require it through use of ids or classes).
Hopefully this will help. If not, then please post the URL to your gallery so that I can take a look and help further.
2. When I save the gallery to the folder for that web page it copies the .html address for the original page into the folder as well.
Juicebox-Builder-Pro will always save an HTML page to the chosen gallery folder. This will be a web page containing nothing but the gallery (so that use can use it to display the gallery on a page of its own).
You can change the name of this HTML file (the 'Index Page Name') on the 'Publish' tab.
Alternatively, you could choose to save each gallery in its own separate folder and then embed the galleries using the baseUrl method as documented here (uploading the complete gallery folders to your web server rather than just the contents).
In doing so, you could keep the default 'Index Page Name' (index.html) as each gallery will be in its own folder and the file will not overwrite any other file. (Having each gallery in its own folder may also help keep things organized, especially if you plan to edit galleries with JuiceboxBuilder-Pro in the future).