Wins only count if you enable auto-save. This is different from the Kongregate version where you can load games and keep playing and have the wins count.
This is the popup you see when you click Save Game:
Make sure to enable auto-save if you want your win to count, like the box says.
With manual saving, it's easy to defeat the AI if you look at what the AI did then load your game and then change your orders to counter the AI's move. When saved games were introduced, if this tactic was allowed it would have invalidated everyone's scores that some people spent many hundreds of hours working on, so games with manual saving don't count.