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.
a:17:{i:0;b:0;s:8:"aperture";b:0;s:6:"credit";b:0;s:6:"camera";b:0;s:7:"caption";b:0;s:17:"created_timestamp";b:0;s:9:"copyright";b:0;s:12:"focal_length";b:0;s:3:"iso";b:0;s:13:"shutter_speed";b:0;s:5:"flash";b:0;s:5:"title";b:0;s:8:"keywords";b:0;s:5:"width";i:896;s:6:"height";i:768;s:5:"saved";b:1;s:9:"thumbnail";a:2:{s:5:"width";i:100;s:6:"height";i:75;}}