According to the rule of least effort, it is highly unlikely that the wind is deliberately programmed to go against you. It's much easier for it to just shift by itself now and then than it is for it to run a check to see which way the character is facing and then to deliberately change direction to go against you. Why would they even put that much effort in to make players mad at them? That makes no sense.

Just go where you want to go. Use the paddle if tacking isn't an option, like in rivers, and consider the wind a gift when it's in your favor. I mean if you're in a river, going slower to avoid rocks and things is a good idea anyway.