This is just to let other people know just in case.
1. I deleted the code from index.php as you suggested.
2. On my php file that I have a powergallery and other jQuery stuff applied, I switched the jQuery library code to the one I deleted from index.php, from the one I had before.
And everything is working perfectly.
I guess other jQuery stuff I had could work with by PowerGallery's jQuery version, so this worked out.
Thank you again for your help, finding out the root problem was the jQuery's version difference was a big hint for me.