I think
@Teban54 is right that this is a problem with Metro North controlling the track.
Here's an interesting post on some of the problems on the line: bad timetabling practices, bad maintenance practices, massive time padding. The new signaling system might be good, but they don't help Acelas if the Acelas still get stuck behind local trains.
From that article, it sounds like MTA is
bragging that Metro North is faster than Amtrak. Really, it should be a giant red flag that the MTA can't manage their tracks to allow for decent express/intercity rail.