As far as I can tell, the 'simulator' does in fact run on rails... but it can get confused by pauses in simulation rate (either by explicitly pausing, or due to poor optimation - hell they know exactly what textures and sounds are going to be needed during ascent... it can't be too hard to ensure that you perform these prior to lift off, rather than at the point of highest dynamic change?
Once it has got itself out of sync the lack of proper simulation calculation>display>perform correction is painfully obvious. How they manage to fudge the rendevous navigation with this sort of simulation methodology I can only guess at, but I think it may not be pretty
( I still find this 'fun' sometimes..... just I usually give up in frustration at basic physics flaws where the cues don't agree with what is happening out of the window.. Doesn't happen everytime, but often enough to put me off.)