Jquery doesn't have any problem with PHP neither other server languages.
Javascript is independent of it.
If the scripts are loaded, they must run.
You just should check if the scripts are correctly loaded (check source code in firefox and click on the js srcs to open: if you see javascript, OK, otherwise there can be a 404 for that script source).
Other problem you could be in is access to the folders where the scripts are.
Other tip is to see Javascript error pane of your browser.