Currently the firmware does skip station runs if the watering percentage is very small and if the effective water time (after multiplying the watering percentage) is very short. I looked up the code and here is the logic:
https://github.com/OpenSprinkler/OpenSprinkler-Firmware/blob/master/main.cpp#L443
If I understand it correctly, you want to accumulate the water time and have the stations run if the accumulated water time is larger than a certain threshold. Is that correct?