When adding or removing items from the Visual Studio toolbox, remember that the last process in wins.  Visual Studio saves your toolbox settings to the C:\Documents and Settings\ <username>\ Local Settings\ Application Data\ Microsoft\ VisualStudio \8.0 \toolbox.tbd file when it shuts down, so if you have multiple instances open (on average I have three), make sure you close the instances that have the unmodified toolbox first.  After closing the others, then close the modified instance; if you don't, you run the risk of loosing your changes. 

As a best practice, I have only one instance of VS open, make the changes, and then immediately close to save.

Optimistic concurrency with automatic conflict resolution - the best of both worlds, right?