When configuring VS2005 solutions under version control you should not check in the binary suo file.
This however is the file that contains the memory of which is the default project.
The only way around this I have found was to move the project that you want to be the default to the top (well the first non directory) of the sln file (In the Project bit). You also need to move the project up the postSolution section to the top of the list.
There does not appear to be any way to control this in the IDE that is not recorded in the suo file.
This is not documented anywhere I can find.
It appears that the default project is the first project added to the solution.