We see a similar issue with Visual Studio 2005 projects that we want to build both for a Win32 configuration and for a number of distinct smart device platform/configuration combinations.
At arbitrary times, every configuration gets auto-generated for every platform, whether it's valid or not, exploding the size of each of our ~50 project files and causing a lot of work to fix the issue.
It consistently happens when we open the Configuration Manager dialog, and it sometimes (but not always) happens when changing a project setting for a configuration. In the latter case, it seems to be related to manipulating the platform and configuration drop-downs on the project setting dialog.
We filed it as a Visual Studio issue; MSFT closed it as "won't fix".
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