When you are using AJAX, the scripts do not get correctly parsed because of the fact that the update panel uses the innerHTML property and you should dynamically evaluate the scripts if you want them to be recognized as such. This is related to the way the MS AJAX Framework works and it is not directly related to the RadControls and RadToolTipManager. However, since the manager loads its content through AJAX in your scenario, you experience this general issue.
For such cases, we have prepared a blog post which explains this problem and also offers a sample solution. The blog post has also attached a demo which reproduces the problem without usage of any RadControls and also has the suggested workaround implemented. I believe that this post will be helpful - you can find it below:
The solution in the blogpost is pretty complex and it does not work in some partcular cases. Another solution is to register your scripts from teh user control's code-behind as explained below:
Please, examine the provided resources, find the better solution for your case and let us know how itt goes.
the Telerik team