I'll assume you also posted this to the MSDN forums since a question with identical text was posted there which I answered yesterday.
http://social.msdn.microsoft.com/Forums/en-US/vsx/thread/96556cd4-44dd-4e01-8198-b83a66c6df26
In short it sounds like you have an explicit reference to v2 of Microsoft.VisualStudio.Shell.dll, James is incorrect in saying you aren't supposed to use this, this is simply MPF from 2005. Referencing it is perfectly fine. If you have an explicit version in the reference in the project file try dropping it, if not try adding the binding redirect mentioned in my MSDN forum post.
I have started a mail with the SDK team about this issue though I don't know if they will be taking any changes this close to release. Also, as an FYI, since Shell.dll is from 2005, it is nearing the end of its supported life, we generally support three versions of previous VS releases.
On release of 2012 the support will be 2008,2010, 2012. I suspect in the next release (after 2012) we may stop including Shell.dll (the 2005 version) entirely in the shipped product. Unless you need to run downlevel on say 2005 I would update the reference to one of the newer shell assemblies (like 9.0, 10.0 or 11.0)