What's the street routing? I'm guessing that it's a problem with street routes, the visual display, or more likely both.
The silver bus should have simply been routed to stop at Chinatown and then take Kneeland/Essex steets to and from South Station.
It certainly doesn't need a direct connection with Boylston (510 feet from Chinatown), and, since it's connecting with the Red Line at South Station anyway, arguably not with DTX either (a more daunting 1200 feet from Boylston in any case).
This surface routing is a bungled mess, and all the worse that it now appears on our half-a-million dollar signage. Yuch.
The worst part is, theres no direct connection from the green line.
From Boylston, youd have to take SL5 to tufts, then board SL4 to south via chinatown.
The entire point of the silver line tunnel was a direct connection to the green line. This fails in every way.