Hi and thanks for the kind words!
I suspect - and this is just a hunch - that the speedbrake does not registers as "completely down", or the flaps are not "exactly" in 1 or 5 - this sometimes happens with hardware "axis" assigned to those functions, instead of buttons or keyboard presses.
To "test" this you could a.) display the values for flaps and spoilers using the "data out" function - it will show you the exact values for those flight controls in green numbers on screeen and/or b.) unassign thoses axis (temporarily) in the setup of your Honeycomb hardware and operate those controls with buttons or key presses (or the mouse in the virtual cockpit) and see if that makes a difference?
Another thing to test is pushing the thrust levers forward really quick during taxi-out before your second take-off - just to test for the takeoff warning - it beats finding out about the problem earlier than in the middle of your take-off run ;-)
Let me know how that works?
Cheers, Jan