The tapestry.js file comming from Tapestry5-jQuery is normally not the same as the one proposed by Tapestry. Just the name is the same.
If you have exactly the same file, you use maybe jQuery AND Prototype at the same time in our application. in this case, you still use the tapestry.js of Tapestry.
To check if you are using the Tapestry version, you can have a look to the javascript files loaded in your page, and if find an prototype.js, you are using the Tapestry version.
Manu