The issue I described here :
http://pytools.codeplex.com/discussions/363287 still occurs from time to time in Visual Studio
2010, even though I have bumped up the value of HKEY_CURRENT_USER\Software\Microsoft\VisualStudio\10.0\PythonTools\Options\Advanced\CrossModuleAnalysisLimit to a very high number.
I can live with this, as it works most of the time.
I have now moved to Visual Studio 2012. On first startup, I see that the issue described above is present immediately. I observe that there is not similar registry key for 12.0.
Is there a solution or workaround for this?