You can minimize the padding by setting all padding configuration options to zero:
stagePadding="0"
imagePadding="0"
thumbPadding="0"
There is currently a 10px separation between the thumbnails and the main image (when the thumbnails are positioned LEFT or RIGHT) which will be removed in the next version of Juicebox-Pro (although I do not know when it will be released).
In a test gallery I created using only the following configuration options:
thumbsPosition="left"
maxThumbcolumns="3"
maxThumbRows="4"
... (all other configuration options at their default values), 4 rows of thumbnails are displayed, even in a browser window of limited height with very little padding between the thumbnails and the top and bottom of the browser window.
Make sure that there are no generalized CSS rules on your web page which the gallery will inherit, for example any CSS rules which apply to all <div>, <td> or <img> elements on your web page (including those within your gallery) which might introduce a margin or padding.
If you continue to experience difficulties, please post the URL to your gallery so that I can take a look.
[Post moved to new thread to keep individual queries separate from each other.]