Failed to load toolbox item. It will be removed from the toolbox

I was suffering from the same issue for one of our applications and could not find a solution. So I created the user and custom controls manually. After searching the web again I finally found why the designer is failing for this particular project. The answer is that project is 64 bit and Visual Studio is still does not have a 64 bit version, it is still 32 bit. So the designer could not load the controls in 64 bit applications or in class libraries. Read Microsoft's article about this. There was an article on Visual Studio web site but it was removed. See the the answer in Visual Studio support forum.

I had the same issue lately. As this (nor any other answer on this site and on the internet) actually helped me, I found out the way to fix it.
Just clean the files and rebuild the solution. As simple as that.

You don't have to necessarily insert the user-control manually. I had the same situation an there was a reason for it.
In my case, it failed because the EXE assembly was compiled to 'mixed-mode' by using CLR support type /clr. After changing it to 'managed-only' by setting type /clr:pure, it worked.
For details, see my answer here at SO.