Visual Studio 2010 randomly says the command line changed, and rebuilds

Visual Studio sometimes decides to rebuild my entire huge project because of one small change. I turned build logging up to Diagnostic to see what was the problem, and here's what I'm seeing:

< Bunch of spam >
Outputs for C:\<snip>\PRECOMPILEDHEADERS.CPP:
    C:\<snip>\PRECOMPILEDHEADERS.OBJ
All outputs are up-to-date.
Forcing rebuild of all source files due to a change in the command line

... and then it rebuilds my precompiled headers, then everything else.

This happens when I change a single .cpp or .h file inside the project. I'm not changing anything in the project settings. It also doesn't happen all the time for the same change; it's random.

Any ideas on what's going on here? Where can I get more information? I tried enabling debugging via the description in http://blogs.msdn.com/b/vsproject/archive/2009/07/21/enable-c-project-system-logging.aspx but it didn't give any more information. I can't figure out where this "Forcing rebuild of all source files due to a change in the command line" is coming from. It's not in any of the factory MSBuild files.

Some other info: it's a C++/CLI dll project that links a lot of other projects, including C#, native c++, and other C++/CLI dll's. I tried removing all the C# projects from the dependencies since those tend to cause problems, but that didn't change it. I've googled that specific string, but my situation doesn't match that of any of the other people reporting it. (One was using Intel C++, another was MSBuild from the command line and changing the case. I'm hitting build solution from within Visual Studio itself).

Edit to explain common fixes I've tried:

I've tried building only the project. Does the same thing.

I'm not including any .h files that don't exist.

I've deleted the bin/object folders and rebuilt from scratch. This usually makes it go away for a couple builds, but then it comes right back.

Edit #2:

Found something suspicious earlier in the log:

3>Using "ResolveNonMSBuildProjectOutput" task from assembly "Microsoft.Build.Tasks.v4.0, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a".
3>Task "ResolveNonMSBuildProjectOutput"
3>  Resolving project reference "..\..\..\..\CommonCore\VS2010\Project1\Project1.vcxproj".
3>  Project reference "..\..\..\..\CommonCore\VS2010\Project1\Project1.vcxproj" has not been resolved.

This is repeated for several of my projects... I'm gonna chase that down and see if maybe it's a problem with the project reference hint paths.

Solution

I did three things, and the problem seems to have gone away. I'm trying to narrow it down a little but I figured I'd go ahead and post them:

Deleted and re-added all the references and project references
Fixed one of my projects that wasn't setting the .NET framework target to 3.5 to match the rest of my solution (I was getting away with it because the project didn't use .NET anyway)
Set "Copy Local Satellite Assemblies" to false for all references including System ones.

Beware that some or all of this stuff might be voodoo...