Yes, I also noticed the exact same thing -- i.e. upon loading the .sit a second time, both the glider and towplane appear on the runway, but, for whatever reason, the towplane decides to take off on its own. In fact, on subsequent loads of the .sit I've even noticed it ground looping...going around in circles!
Well, thanks again for all your help--.at least now we know that the issue can be easily reproduced.