Scripts called with ?ver=3.4.1 ending and jQuery $ is not a function

Hi,

I have a problem when activating the YAK for WordPress plug-in.
The jquery $ is not a function problem happens, with three scripts:

fadeinout.js:3TypeError: 'undefined' is not a function (evaluating '$(document)')
common.js:1TypeError: 'undefined' is not a function (evaluating '$(document)')
jfancy-custom.js:6TypeError: 'undefined' is not a function (evaluating '$(function () {

	$('#slideshowHolder').hide();
	var slidenos = $('#slideshowHolder').length;

})')

The thing is I tried by using this:

(function($) {
// your code with dollars here
})( jQuery );

The problem is that when I make the changes, the same problem happens and when I look at the files from the error console, the files remain as unchanged.

The two files: common.js and fadein out.js are being called like this:
/wp-content/themes/echoes/js/fadeinout.js?ver=3.4.1

So I believe the problem is the thing after the script name: ?ver=3.4.1

I think this causes WordPress to use another script, not the one that is actually on the folder.
Where is that script? How do I change it?
or What can I do?

Thanks in advance!