I have pushed two separate fixes for the signalling in the last few minutes. I am not sure that this will fix all of the issues, but I should be grateful if you could let me know how it works now.
Incidentally, I notice that you often place starters beyond the ends of platforms: starter signals should be placed on a platform tile for them to be recognised as starter signals, holding the train in the station, where it can continue to load, until the route is clear.
Edit: It is difficult to tell what is caused by a bug and what is caused by the use of multiple station signals with the current arrangement.
Edit 2: The arrangement of signals that you have will always cause trains to travel slowly on most of your single line sections, as the trains will have last passed a signal protecting a junction (the exit from the passing loop), and signals protecting a junction will always be in either danger or caution, meaning that trains passing them can only travel at half line speed.
Is this the issue that you are describing?