Just tested your file against the Comskip in 2.4.6 vs that in 2.4.7 and it runs at exactly the same speed about 25fps. That the default speed of the free version of Comskip for mpeg4 files. There is no change.
I guess there’s something changed in your configuration. If I were to guess I’d say you accidentally set your MCEBuddy priority to low. That’s the only thing that can cause that kind of slow down, either that or your file is heavily corrupted.
On a side note the donator version of Comskip ran at about 400fps on your file.