Hello,
the problem might be in the paths of the corresponding JS scripts, that may not be correct when SEO is on.
Often there is problem with relative VS absolute paths, as with activation of SEO a virtual directories may appear.
So if you would be loading a JS scripti using ./js/somescript.js, it may work fine at URL mydomain.com, but it will fail when the URL changes (thanks to SEO) to mydomain.com/cat1/product1, as there exists no js folder at this virutal level.
This is the most probable source of your problem, so, please, first of all check if all the paths are correct regardless the "current" URL.