It seems to me that overriding the next station with Smarter Trains mod fails in certain situation.
Based on my testing, the problem is triggered if the next station in the line is full (meaning it has train limit set, and no free slots for more trains). In this situation the train selects the next stop in the line, even if the line rule says to go to a different station instead. Attempting to use the signal lamp to redirect train to different station does not help -- the result is the same: If the next station in line config is "full", that station is selected.
Also, is there a limit as to how many stations can be on a line? I tried working around the issue by having extra stations on the line, but once I got something like 20 stations I started to get assertion errors when clicking save on the train line. However, this issue is not major. If the original problem can be fixed, I don't need more than dozen stations.. :)