Yes this is a game issue, I have noticed this many times.
Another thing that happens is for example I saved the game with 15mps winds and high waves, then next day started again at the same point, only to find that the wind was still 15mps but the waves were only as one gets with 4 or 5 mps.
After playing for a while, it gets back to how I left it.
I think this is a game feature rather than a fault with your system.
