So, an FYI for all the users who did not know this. With ver 1.3.1, you are able to a specific "Select Image" for the thumbnails you wish to regenerate. For example, I wanted to regenerate my "Facebook New" size that I had assigned to my products and categories.
I chose "products" from the "Select Image" drop down menu and hit Regenerate Thumbnails. When I received a server timeout error (most host providers will have a timeout limit for security reasons), I unchecked the "Erase Previous Images" box, and Regenerated Thumbnails again. I had to do this a few times before the operation was completed successfully, but it worked in the end.