Recently I faced a javascript reference issue in my application. I had javascript file referenced in my master page. I had given relative path to the JavaScript files.
<span style="font-weight:bold;"><script type="text/javascript" src= "../../Script%20Library/jquery-1.4.2.min.js"></script></span>
It was not working for all the pages across application due to different hierarchy.
So below dynamic reference style can be used to overcome this issue.
<script type="text/javascript" src= "<asp:Literal runat='server' Text='<%$SPUrl:~sitecollection/Script%20Library/jquery-1.4.2.min.js%>'/>"></script></span>
