I don't know what's wrong with your pause. I would save and back up my save files, then re-install and copy the save files back in, in that situation.

As for farming, I believe watering the crops is pretty much the same as "Studying the medicinal cactus" or "Fixing hut". Pretty much a practice task to use to make skilled farmers, even when there's no food to harvest. It doesn't change the time until they sprout, and I don't believe it affects the yield, either.