Yes, phpThumbOf has a few face-palm-worthy moments when it comes to performance.
Because of its dumb attempt at cache cleaning, the more images in your cache the slower phpThumbOf gets. On sites with a few thousand cached thumbnails this can add several seconds to the generation time for each page, even if phpThumbOf doesn't need to create any new thumbnails. Every time the snippet runs it tries to clean its cache. (And the comical irony is it never even
deletes any files, just wastes time.)
Also if you use the same image on multiple pages—for instance a banner image on each page in a given section—phpThumbOf will create a separate thumbnail for each page. This exacerbates the cache cleaning problem, plus it means visitors have to download the same image—just with a different name—each page they visit.
Have you looked at
pThumb? It's my effort to create a faster and more robust phpThumbOf. On most sites you can simply uninstall phpThumbOf, install pThumb and be done, with no changes to templates or chunks needed. I think you will notice the difference in speed.
Although resizing a 116 megapixel image is going to be slow no matter what. That is a massive image.
Also, your server would benefit from a newer version of PHP. 5.3 is reaching end of life, and newer versions improve performance and memory usage
considerably.
If you don't want to mess with anything new, at least go to System Settings, core > phpThumb and set
phpThumb Max Cache* (3 settings) to 0. That will cut phpThumbOf's cache cleaning attempts short.