I was having an issue where the Apple Watch wouldn't recognize times that I would stand (or have other activity) in the Activity app. After trying everything, I finally reset the watch ("erase all content and settings" in the Watch app). After setting up the watch (as a new device) the watch hasn't messed up once in reciting "stand" data. Give it a shot...
At the very this makes me think that the problem is a software one which can be fixed with a software update down the road.