Would you please provide more details about your configuration - is the user control directly in a separate tooltip or you are loading it on demand with AJAX? If you are using AJAX, please note that in this case 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.
For such cases, we have prepared a blog post which explains this problem and also offers a sample solution. The blog post has also an attached 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 particular cases. Another solution is to register your scripts from the 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 it goes.
the Telerik team