As Juicebox and SimpleViewer use different platforms (HTML5 vs Flash), Juicebox was written from the ground up (rather than simply being an HTML 5 translation of SimpleViewer) and the two image viewers feature slightly different feature sets.
The icons in a Juicebox gallery are actually characters in a custom font.

You can change the size of the navigation button icons using the navButtonIconSize configuration option (in JuiceboxBuilder-Pro's 'Customize -> Main Image' section). You can also change the color of the buttons using navButtonIconColor, navButtonIconHoverColor and navButtonBack Color ('Customize -> Color').
Please note that this will affect both the main image and the thumbnail navigation buttons. (There are no separate options for each.)

If you want to change the icon itself, then you would need to either edit the character in the font or choose a new one (and then generate a new font for use in your gallery).
Please see the Using Custom Icons support section for details.

It's hard to know what might be wrong without seeing exactly what you are doing. It should certainly be possible to edit or replace a couple of icons at once.
If you upload the updated zip font file that you've created in IcoMoon somewhere (either your website or a file sharing service such as Dropbox) and provide a link, I'll take a look and see if I can find anything amiss.
Also, please let me exactly know what you are trying to do: whether you are editing or replacing the previous and next icons and, if you are replacing them, what icons are you trying to use (please let me know their codes).
Once I know a bit more about what you are doing and can see your customized font for myself, I should hopefully have a better idea of what the problem might be and how to solve it.
Thank you.