Thumbnails in a Juicebox gallery are always the same size as each other.
In a Juicebox-Lite gallery, the thumbnails are all 85px x 85px.
The images are scaled to fill (not fit within) the thumbnail dimensions so, if the images have a different aspect ratio to that of the thumbnail dimensions, cropping will occur.
With Juicebox-Pro, you can change the thumbnail dimensions via the thumbWidth and thumbHeight configuration options (see the Thumbnail Options) but please note that thumbnails will all still be the same size as each other.
I hope this helps to explain what you are seeing.