That may not be a practically relevant difference. Why would you want to run F# on the JVM? To interface with JVM code. IKVM lets you do that already.

I've rolled out multiple .NET programs that contain Java open source libraries through IKVM. It works just fine, and the amount of extra work you need to do to make the JVM->.NET mapping work is remarkably little.

Or perhaps you'd wish to run F# on the JVM because you like the language, but don't wish to depend on .NET (or Mono).