It sounds like you might need to reduce the maxThumbColumns from its default value of 10 to something smaller (such as 3). (The default value for maxThumbColumns is 10 as this is an ideal value for the default value for thumbsPosition of BOTTOM.)
When setting thumbsPosition to either LEFT or RIGHT, Juicebox-Pro uses the maxThumbColumns value as the actual number of thumnail columns and the number of thumbnail rows is variable (up to the maxThumbRows value) depending on the space available within the gallery.
Also, space is reserved in the gallery for the thumbnail area and the remainder of the gallery area is used for the main images. (When setting thumbsPosition to LEFT and maxThumbColumns to 10, the 10 thumbnail columns are displayed leaving little or no space for the main images in a 'regular' size browser window.)
The maxThumbColumns configuration option can be found in JuiceboxBuilder-Pro's 'Customize -> Thumbnails' section.
I hope this helps to describe what you are seeing and resolve your problem.
Please let me know how you get on and if I can be of any further assistance.