+2  A: 

Sorry if this ends up being completely off-base, but I remember running into something like this a while back. I fixed it by adding 'defer' to my script tag, i.e.:

<script defer="true"> ... </script>

This prevents the script from running until the rest of the page has finished loading, which avoids an IE DOM bug that sounds very similar to what you're getting. I haven't used ASP, though, so I don't know how you would add the defer attribute through ScriptManager.

DNS
Thanks for replying, I actually read that solution before I posted here, and tried it. However, the script never got rendered to the page when I added it. I'm guessing it doesn't work with ScriptManager/updatepanel.
It Works (TM)! Had the same problem (a jQUery plugin was trying to run before DOM was ready).
Piskvor
+2  A: 

This looks like a case of the script modifying the DOM before it has loaded. If I were you I would look at adding the script when the DOM is ready. Plenty of JS libraries have ways of doing this.

More information on this sort of error: http://blog.mjjames.co.uk/2007/11/knowing-whats-on-your-page.html

MJJames
A: 

I've come across this problem as well. I found it affects IE6 and some versions of IE7 as well. In my case the problem was actually being caused by the ScriptManager.RegisterStartupScript method. Once I removed that it worked fine

Phil Hale