JuiceboxBuilder-Lite and JuiceboxBuilder-Pro use the same methods for resizing images for thumbnails (and Juicebox-Lite and Juicebox-Pro use the same methods for displaying them in the gallery). The only difference is that Juicebox-Pro allows you to choose the thumbWidth and thumbHeight parameters.

JuiceboxBuilder-Lite and JuiceboxBuilder-Pro have always cropped images to fill (rather than to fit within) the chosen thumbnail dimensions.
I am not familiar with IMatch or its Juicebox plugin. Perhaps it scales the images differently that JuiceboxBuilder does when it creates the thumbnails for the gallery.

Maybe if you could post links to the two galleries that you are referring to (the Lite one that's OK and the Pro one that's not), I might be able to figure out what's going on. Thank you.

Also, there are a couple of workarounds that you might like to try:
(1) Upgrade the IMatch plugin from Juicebox-Lite to Juicebox-Pro by swapping the plugin's Lite 'jbcore' folder for the Pro version from your Juicebox-Pro download zip folder ('juicebox_pro_1.4.3.2/web/jbcore/'). The plugin should still use the same resizing algorithm as before and all galleries subsequently created by the plugin will be Pro.
(2) If you create your gallery with JuiceboxBuilder-Pro, you could swap the thumbnail images (in the 'thumbs' folder) for a custom set of your own (created by a different program).

Unfortunately, there is not a scale-to-fit option for the thumbnails (only scale-to-fill), although you could certainly suggest this as an idea for a future version in the Feature Requests forum thread if you like. (The thumbnails were designed more as a navigation tool than as a method to showcase the images themselves. The main images can be scaled to fit within the gallery's image area (in their entirety, retaining their aspect ratios and without cropping) by using either imageScaleMode="SCALE_DOWN" or "SCALE").

I'm glad you've found a suitable workaround for your problem.

Yes. Juicebox contains its own bundled version of jQuery so that no other dependencies are required. A user can just

The 'juicebox.js' JavaScript file is packed and obfuscated and cannot be modified so it would not be possible to remove the jQuery content from the file. Also, one benefit of Juicebox using its own version of jQuery (other than not having to ensure that jQuery is included in the web page containing the gallery's embedding code) is that we can be sure that all Juicebox functionality works OK. If a version of jQuery older than that required is used or a bug is introduced into a new version of jQuery, the gallery may fail to function correctly. Juicebox using its own bundled version of jQuery avoids this possibility.

@borut.podlipnik

You can change the shape of the thumbnails with thumbWidth and thumbHeight (via the 'Thumb Width' and 'Thumb Height' sliders in the 'Thumbnail' control panel). They do not need to be square but they will all be the same size as each other.

The thumbnails exported by Lightroom are not cropped (as you have discovered). Lightroom uses the thumbWidth and thumbHeight values as maximum bounds when resizing the images and their aspect ratios are respected.
However, Juicebox will always dynamically scale the thumbnail images to fill the thumbnail dimensions (with cropping if the aspect ratios do not match) when the gallery is displayed.
Even though JuiceboxBuilder-Pro crops thumbnails to the exact thumbnail dimensions and Lightroom does not, if you view galleries (built with JuiceboxBuilder-Pro and Lightroom) with the same thumbWidth and thumbHeight values, the galleries (and thumbnails in particular) will look the same.
There is no way to change this.

The only thing you could do is create your own set of scaled-to-fit thumbnail images (in Lightroom, Photoshop or another imaging program) and replace the ones in the 'thumbs' folder.
Please bear in mind that it would still not be possible to have thumbnail images of different sizes. All thumbnail images will be displayed at the thumbWidth and thumbHeight dimensions. If you have images of varying aspect ratios, you may need to pad your thumbnail canvas with blank space (at the top and bottom or left and right) to fill the thumbnail dimensions.

If you like, you can post suggestions for future versions in the Feature Requests forum thread.
This keeps all the ideas together and ensures that they are not overlooked by the developers.
I do not know the likelihood of any suggestions being implemented but this is certainly the best place for all ideas.
Thank you.

OK. I found "Juicebox Feature Requests".