I had been really bugged by the way VS.Net 2005 seemed to treate project references.
As I mentioned in a previous post, if you remove a project from a solution, all references to that project are also removed from their respective project.
The result is that lots of project suddenly lose reference to a needed dll or project, and you have to go back and manually add the reference back in. Big pain.
Thankfully, Mikhail Arkhipov from Microsoft has reassured me that 1) I am not going crazy, 2) this is not by design as in fact a bug, and 3) it will be fixed in a (hopefully soon to be released) service pack.
Strike 1 issue with VS.Net 2005. Only like 10 more to go.