Rhino only allows a single assembly of a given name to be loaded in the process. When the .NET framework tells Rhino that is needs to find an assembly, Rhino walks through the list of directories where every plug-in is installed and attempts to find the DLL in that location. I’m guessing Rhino is looking in the older plug-in directory and loading the fsharp DLL from there.
I don’t currently have a good fix for this.