Hello!
I once had a problem with a user control I added twice in the same page. In my case, the javascript functions didn't know which control to refer, due to the fact that I had the same ids in the user controls and the javascript only wokred for the first control.
I solved the problem by changing the controls' ids and by changing the javascript function to look for the client id of the control, e.g.:
<br />
document.getElementById("<%=ControlName.ClientID%>")<br />
Hope this helps a bit!