It's possible that the change is a result of TF2 being altered in one of the recent downloads.. even some of the comments in the interview linked above indicate Valve has done a lot of work 'on the back end'. Have you tried a previous version of the map running on a current version of TF2 to see if the behaviour is the same or different?
No, I haven't tried that.
Here's something I noticed though. The whole cart is the func_tracktrain, where I've read other people just make one nodraw brush - tie that to tracktrain, then parent their collection of brushes that make up the car/train to that moving nodraw brush. I wonder if that's where the difference - as in if you did it that recommended way, you'd get the car moving out from under the floating sentry.
I think that maybe the case, because I know when I first started and tried to make this, I did it like mario, where I had a box car all tied to the func_tracktrain and I didn't have the problem where the sentry floated in place - instead, I was never able to build the sentry to begin with. It looked like it would have been able to build though, if the blueprint thing wouldn't stop jumping back and forth real fast, skipping around like the refresh didn't match the speed of the moving train.
I notice that's the same thing that happens on this mario, the blueprint jumps back and forth. Except in mario you see it flash from the red x telling you you can't build there to the outline showing you can and if you hit the left mouse real fast you can end up putting it down when it's just at the right time and it sticks. (hope this makes sense - you may have to try it to see).
I wonder if the speed of the train on mario is just closer to being in sync with that blueprint refresh. I maybe far off, but that's what it looks like to me.