Having cropped images (most likely square) even in the lightbox is a telltale sign of a theme developer's bad practice. WordPress has a few built-in image sizes, of which JIG uses the "large" version. When you upload an image, this size is automatically created. It's good in cases when the uploaded image is way too big for web. However, if you carefully craft your photos to upload to be web-sized and optimized, the "large" version is often useless. In this case, themes can re-define what "large" is and make it a force-cropped small square - for whatever reason. You can choose what size JIG uses for its lightbox target and a source for the thumbnails (then it generates smaller versions).
Go to JIG settings > Lightboxes tab > Maximum size for lightbox (the image will link to this size) and set it to Full - this should solve the cropping issue, but make sure your source image is appropriately sized.
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