It sounds like your gallery is not using your thumbURL images for your thumnails.
If the thumbURL images are missing from your web server (or the paths to them are incorrect in your gallery's XML file), Juicebox will use the imageURL images instead but these images are not scaled to fit the thumbnail dimensions when the gallery is displayed. (They are center-cropped as you describe.)
When creating a gallery with JuiceboxBuilder-Pro, your original images are scaled to generate dedicated thumbnails at the specified dimensions. However, when the gallery is displayed, the images used for the thumbnails (whether they are the thumbURLs or the imageURLs) are displayed at actual size (as the dedicated thumbnails should match the thumbWidth and thumbHeight values and this should not be a problem). This has been logged as a bug and should be fixed in a future version of Juicebox.
Check the that your thumbnail images are present in your gallery's 'thumbs' folder and make sure that the corresponding thumbURL entries in your gallery's XML file are correct.
If you continue to experience difficulties, please post the URL to your gallery so that I can take a look and help further.