You can see where FSI is located by typing
System.AppDomain.CurrentDomain.BaseDirectory;;
In my computer I get
C:\Program Files (x86)\Microsoft SDKs\F#\3.1\Framework\v4.0\
And I have a file
Fsi.exe.config
which does the redirects.
You probably point to an old FSharp installation, as 4.3.0.0 and 4.3.1.0 should be binary compatible.