Update: I’m still having many issues with the Gallery shortcode. I am using the size presets for big preview and as soon as a select “No, do not force the same size”, the image expands to some undefined size with low resolution. It has worked on one entry here: http://www.pixal.ca/portfolio-item/rowan-elshabassy/, but on no others. The gallery function is being very inconsistent.
After more debugging, I found script remnant from a plugin I installed ages ago. It was blocking the theme’s script. I’ve also dealt with the thumbnails. From what I can tell, simply selecting the number of columns that constrains the thumbnail size to something small regardless of how many images I have does the trick (e.g. A gallery with three thumbnails uses 7 columns to generate a smaller thumbnail size).