This appears to be an old bug: http://social.msdn.microsoft.com/Forums/en-US/msbuild/thread/8a2f4af8-7a57-454f-aa7d-684f3f89acf3/
Here is the reply that was given by Microsoft when this was first reported:
It looks like you've revealed an interesting bug in the Visual Studio (C#) project system. This is not an MSBuild issue specifically. It turns out that the project system temporarily renames the XML file until the end of the build, so there's no way to access the doc file by its actual name during the build. (Note: even the "AfterBuild" target is still technically part of the build).
This is an IDE-only problem, and you should never see this on command-line builds.
--Sumedh (MSBuild Team)