Understanding Publish Compatibility Check failures
Yishai Galatzer wrote an informative blog post about what to do if you see errors in the Publish Compatibility feature of WebMatrix. May be relevant to you if you use Web Deploy protocol to publish from WebMatrix: http://blogs.iis.net/yigalatz/archive/2011/02/04/compatibility-checking-in-webmatrix-when-the-checker-reports-failures.aspx