Does it work if you do this:
Create a new C# Windows Application in a new solution (don't use a solution folder)
Add a user control
Build
Open Form1 in the designer.
If this does not work, can you check your options at Tools->Options->WindowsForms->AutoToolboxPopulate?
Another thing you can try is to reset your toolbox (right click and choose "reset toolbox"). There might be some old tabs that are intefering with the feature.