JCR:

Every time I switch back to H9 Control it is showing the H9 is connected message which has to be accepted. Although the two bluetooth leds are lit on the H9 al the time is there a change the H9 Control app looses the connection to my H9 when focus is set to forScore app?

Yes, when you leave H9 Control and go to the forScore app, H9 Control quits.  So, it's no longer listening for MIDI messages from forScore and sending them to the H9.  We intentionally disabled background operation for H9 Control because it was causing strange bugs and there didn't seem to be much reason to enable it since H9 Control starts very quickly.  I guess I'll have to take another look at enabling background operation to see if I can figure out where the problems I saw were coming from.

JCR:

But I can't get it to work on the Windows version of H9 Control either. 

Hm.  It works fine on my Mac, but I don't think I ever tried it on Windows. I'll have to see if I can reproduce the problems you experienced.