I have had this problem even before TANE SP2 and the hot fix.
I have solved my problems in two ways. First make sure the speed is reduced when approaching the station, maybe 35 mph or less. But the other thing that helps solve the problem is to increase the max-decal in the engine spec. Open up the locomotive asset for edit and scroll down until you find the engine spec kuid. Once you have found the engine spec kuid you can now revert it back to the original. Now open up the kuid for the engine spec and scroll down until you find the line max-decal. Increase the number (for testing purposes to see if it solves my problem I usually just double it - you can come back and fine tune it later). Submit the edits and test your route to see if the train now stops at the station. These two things have solved over 90% of my station run by problems.
The engine spec fix may not be very prototypical but it works for me.
		
		
	 
Well now, you may have stumbled on a fix or work around to the problem. (Than you!!)
I changed parameters to the engine spec as you indicated, and now that railcar stops at the platform.  It has to do something about inertia of the vehicle.  The "bad" platform was one of these of 20' long.  And if the loco arrives at more speed that it is able to stop, looks like it does not trigger or acknowledges it has arrived, and overshoots.  Make the loco to stop sooner and it does!
So, using the same principle of inertia, I look at my track marks and reason that if the radius is set to a minimal distance, the loco may not have enough time to trigger, and may overshoot.  So I set each trigger to minimum one meter radius, and now in the brief test I made, where a loco would overshoot, now it doesn't!  Is important to differentiate here what are you using the track mark for:
Drive to.  Radius is important because you have to give time for the loco to go over it and stop.
Drive via.  May not be so important because the loco will pass it and continue to the next task.
Same for Navigate via or to.
Because you don't know what command is given to each track mark, is better to set them to a minimum one meter radius.
On platforms and stations, you can't adjust the radius of action ( or I am not aware of how to do it), so you have to play with the speed of the consist so that by inertia it does not overshoot, hence adjusting the parameter of DEC (eleration) so it stops before running off the platform.  This is why 20 and 10' industrial tracks may present more problem (You may think the developers could have made some changes as to the required speed of a loco or consist entering these).
Another uncomfortable aspect of all this, is that things may run well on the first run and deteriorate as time goes by or after a save session (I can't explain why).
What I have stated here, in reality should have made public time ago by the authorities.  Or it gives us to think the problem is not important enough and we have to bang our heads to reason and come up with workarounds.
Of course I may be wrong with all this, and people may still have problems.  OH, well! I tried...