Please confirm that you have edited the right copy of the user control, and it is actually the one defined in the <toolboxControls> section in the application web.config
Sitefinity always takes the custom user controls from the file system so the last change should be reflected immediately after it's made.
We apologize for not being able to help you further, but we see no way to replicate this issue. If you still experience this problem, please provide the exact steps we should take to see this behavior.
the Telerik team