Pokemon-go – For Pokemon Go, the near by pokemon box doesn’t update. Just stays the same. Everywhere

Borrowing from @Codestrife's answer here

The rustling leaves usually indicate that there are pokemon near that area. Going and walking around near that area gives you a higher chance to encounter Pokémon.

Keep an eye out for rustling leaves, hinting at where critters may be lurking and simply hang out in a suspected region for the increased chance of an encounter. - Source

Therefore, the reason you don't always see Pokémon in rustling grass is because there is only a higher chance to encounter them there and not a guaranteed chance of encountering them. You just have bad luck when you don't encounter them.

Thank you for your answers @TimPenner @KevinTian. I actually found a neat way to get around this when I was browsing Reddit.

There's an app called Caffeine which prevents the phone from going to sleep (lock screen) whenever a certain application is in use (Pokemon Go). Instead it dims the screen after the timeout period that usually would cause the phone to go to the lock screen.

So now when I go jogging and I put the phone in my pocket it will stay on indefinitely plus it dims the screen after the 1 min timeout period to save battery.