Not the perfect fix, but I figured out where you can at least manually change the thumbnail dimensions until a better solution is found.
Open the database and find the table [prefix]-ngg-pictures. Find the image(s) whose thumbnails need adjustment. In the meta_data field, you'll find the thumbnail dimensions listed at the end of the meta_data string. Change the width and height to the correct settings and commit the changes to the database.
Worked just fine for the thumbnails I was having dimension problems with.
Hope this helps someone else.