I think it is similar situation to http://forum.simutrans.com/index.php?topic=15765.0
It all applies to 3-aspect choose signals. Weirdness appears when the train is not scheduled to stop in the station ahead of choose signal, and the path out of the station is blocked. In that case, the train should enter the station (choose signal at caution).
But what really happens is, that the signal stays at danger, but the train passes through, not making any reservation to next signal. See http://server.exp.simutrans.com/screenshots/simscr20.jpg
the tank train on top left is just about to drive through danger (and it really did).
It was followed by DMU, which did the same - I have captured more screenshots: 21- 23. Notice that as it approached the next signal one tile of reservation just in front of signal appeared.
The next train (shot: 24) was lucky, and got his reservation through the station - choose signal correctly shows clear+alt route, but look at the right side - signal ahead of DMU is also at clear, although the DMU is waiting for clearance.
Further on (shot: 25), another DMU came, but this time it got clearance to enter the station, just the choose signal was showing clear instead of caution. But the reservation was OK. However it was errorneously change to clear+alt, when reservation through the station was granted. (shot: 26)