What you saw is what I would expect to happen. As I mentioned in an earlier post in this thread, if you go to the menu and change players, then change the game speed before you click Play, the game will ignore that you had it paused all that time and update all of your fishies at the new speed setting when you click Play. Basically, the game doesn't know you had Stop Time set, if you change it to something else before you click Play (and your fish will be in the same condition they would have been if you'd left it at that speed setting when you last saved the game).
You
must click Play immediately after switching players if you want to preserve your game speed setting (whether that's Stop Time or any other game speed setting). Once you've clicked Play, you can go back to the menu and change the game speed.