I've noticed that on all Acela runs I've tried, I get a stop signal at Tower 1 on the ATC even though the wayside signal shows slow approach. Also, when coming in to Providence, I get a stop signal on the ATC before I can hit the stopping point on the platform. On some runs, I'm slowed to restricted speed by the ATC before arriving at Route 128, only to have it change to a clear once the doors are closed. I'm assuming I'm not the only one experiencing this, right? (I did a cursory search and didn't find anything. Also, I've not been on in a while.)
The recent update to "fix" some signalling issues on NYT has resulted in adverse effects for both BPE and HAR. It has been previously noted: https://forums.dovetailgames.com/threads/patch-notes.68977/ I have yet to see any indication from DTG that they are aware of this issue. I have also not seen any explanation as to why a patch for NYT had to be applied to BPE and HAR in the first place, since they already worked as well as one could reasonably hope for a TSW product. I would not expect any information, much less a fix, to be readily available. For now the only solution is to turn off ATC on BPE.
You are not the only one experienc. I reported it as a bug and am currently responding to the person on my support ticket. This bug is actually somewhat realistic though as it is an actual bug in the real life safety system, however under different circumstances! In real life, this flaw in the system happens when your signal drops from a clear to a stop signal and it immediately penalty brakes your train. The response to this in real life is to contact the dispatcher and wait for permission to proceed. Many of the fixes on that list aren't actually functional in the game which is sad. One of them for example is the fault mode when the ATC is "turned off". In actuality that fault mode goes to 79mph when the ACSES system has a fault. When the ACSES system fails it actually brings the train down to 59mph, however for the ATC I have no idea if it does the same, but am guessing so!