Yeah, that's the problem with spellcheckers and grammar checkers. Often if you miss a word, or substitute one word for another (such as you're/your and the like), the program still sees it as a valid word choice and doesn't mark it incorrect. That would require something far more cognitive than an algorithm or program or whatever it is. Not to mention that the grammar checker in Word is often incorrect in what it wants to change. Or at least it has been in my experience.
The best grammar checker is your own brain. And if you still miss a word or a letter, there is always that nifty little "modify" button to use.