A re-install fixed this, although the problem has come back, I don't think that I mentioned either that with the APU on, neither engines will motor (switch next to throttle) I think its a bug, I also am inclined to think that it has some connection with TARS, as I tabbed out, took TARS off standby or enabled the plug-in on Teamspeak (whatever) and then the problem started again.
today I have done many re-installs and this has not solved the issue, its definatly not me or my flightstick as I frequently start up and fly with others.
I'm going to remove all the engine start/stop bindings, re-install then see what happens, I'll do this tomorrow and post the results in an edit to this post.
The re-install has fixed nothing, the engines won't even motor :'(