You can make a permanent fix for the hint path needed to find
FSharp.Core.dll by editing the template in
C:\Program Files\Microsoft Visual Studio 9.0\Common7\IDE\ProjectTemplatesCache\FSharp\Silverlight\SilverlightLibrary3.zip\SilverlightLibrary.fsproj (and probably the version of the file in
C:\Program Files\Microsoft Visual Studio 9.0\Common7\IDE\ProjectTemplates\FSharp\Silverlight\SilverlightLibrary3.zip just to be certain).
Proof of concept -- my orrery-clock upgraded to Silverlight 3.0 (with all the source bundled into the .xap file) here.