I believe the code for handling sensors is exactly the same between 2.1.9(0) and 2.1.9(3). I double checked the two versions source code and didn’t see any difference. So I can’t explain why it makes a difference on your side. I will do some additional test of 2.1.9(3) on flow sensor, but I’m pretty sure I’ve tested it before and it works fine.
Regarding flow count at the end of each station run vs. the type=fl: they are not the same: the former is recorded at the end of a single station run, the latter is recorded when the program queue is empty (i.e. all stations finish running). It’s possible that the former is 0 (because it didn’t register any click during the station run) but the latter is not 0.