My one major complaint is this as well, my 4 year old plays directly above my theater and lately I have had to adjust the focus and make sure the projector is still aligned properly EVERY time I turn it on now! Getting annoying, I turn it on and it's all blurry and then you have to adjust from the unit and you know you can't get it friggin perfect because you aren't at the screen. My w10000 was so much more solid with auto focus and never had this issue. This projector really is great except for this issue. Not sure how to correct it or if its even possible.
I use the true depths and they are perfect, I've never lost sync.
Like Charles mentioned, the projector will be out of focus when first turning it on which is how my unit is as well. Focus the projector after it has been on for at least 30 minutes or more and you should not have to touch the focus after that, but it does require a warm up period before the focus is fully up to speed which I agree is annoying. My JVC also has a warm up period for optimal focus, but the degree my 40/45 are out of focus when first turned on is much less vs the 7000.