The same often happened when I travelled by train in Ontario (Canada) where the trains shared the line with freight service, and so sometimes a train was poorly timed such that it always had to wait for freight to clear first. In those cases, if a train was delayed, the delay occurred at the station such that by the time the train left the station, the freight had already cleared and the time spent on the train was less than it normally would be. Also, delays often meant the train had fewer passengers, so it would stop for less time at each stop... am I on the right track? ;-)
The freight reason is not it. If the freight got out of the way at the same time it normally would, you would decrease your travel time, but arrive at your destination no earlier than a normal arrival.
The second reason is closer, but not exact. Caltrain has a variety of different types of trains, some stop at all the stops, some stop at only a few. Here's the scenario: there is a fast train then a slow train. Your normal schedule doesn't allow you to get to the station on time to take the fast train, so you normally take the slow train. If both trains are behind schedule, you might be able to make it to the fast train, and since it goes faster you might get to your destination earlier than normal.
The frustrating thing of course, is that even if the trains are severely delayed, they have (or had, depending on whether they go out of business soon) a policy of running the exact schedule for each train as if normal. So even if all the trains are piled up, delayed, they would make local stops, etc. even though everyone wanted just to get to the end by express.
Sad that this kind of issue was so common (1x per month at least) that I blame them for not having efficient accident backup plans.
Yes, yes, I realize that there's the problem of having trains go express when they're all stacked up.
