Hi, This jzamora!
I did this example to show something, maybe this can solve someones problem:
I saw one interesting thing on master pages. you can call a .js file from your master page like this:
<script language="javascript" type="text/javascript" src="Script/TestScript.js" ></script> :: the script is in folder "Script"
Then, i created a button and added the funtion event to it like this:
<input id="Submit1" type="submit" value="Press the Button" onclick="testPopup()" /> :: testPopup() in in file "Script/TestScript.js"
Case 1: if you create an aspx web page in the same directory as the master page, javascript works well
Case 2: if the page that is using tha Master Page is in a sub directory like /OtherPages/MyPage.aspx, The inherited page is enogh capable to understand where is Master Page, BUT, right there, Master Page is not capable to resolve the javascript URL, so, Master Page thinks javascript file url is src="Script/TestScript.js" and it should be src="../Script/TestScript.js".
This create a big issue in managing javascript Url on subdirectories. I recommed to create varios Javscript files, with different urls in master page, so any page in subdirectories can call them.
then, is good practice to create various .js. Ok, if U are using various, try to define specific functions and javascript programming for subdirectories only, or general files for all folder levels.