I am having this same problem - some of my custom server controls will not appear in the toolbox, and some of those that do appear will not actually work (as in, they cannot be dragged onto an aspx page).
I think this has to do with the type of base class that I am inheriting from. I'm extending some of the Telerik controls, and those that inherit from their controls that do not inherit directly from a stock asp.net control suffer this same problem.
A workaround would be welcomed as this is a prety serious problem for me.