You are correct; clock messages have no channel. They are also just one byte.
SND F8 09
just sends one clock 'tick' - the '09' is not valid (it's also not a channel number) but MidiFire will send it anyway (which it shouldn't, but that's another topic). I am at a loss to explain why this would have any effect!
I would suggest putting in an Event Monitor and capturing exactly what events quantiloop is sending before any conversions. It should send FA (or FB), a bunch of F8s and finally an FC as the transport is started and then stopped.