Just try restarting the Kindle.
If that doesn't work it's not the scripts.
Yes the scripts are bad, it was more of a proof of concept for me and I think it makes things much worse.
I do like the progress bar remover script though.
I don't even notice the black flash anymore and I kind of like it, as if you look away from the book for a split second and change the page you don't know if you actually switched the page and the black flash makes the page turns more noticeable for me.