I've wondered about this myself. There may be some conditions under which the mix stir could cause head problems: low hop, low protein beer that is mix-stirred and force carbonated with shaking? I don't know what the limit is, but it seems that the mix stir itself isn't going to give you problems on a regular beer, i.e. there seems to be enough protein to go around.
I have had problems with head retention even without using the mix-stir. The yeast was healthy, water chemistry good, temp controlled, etc., but still would get a very low-foam beer on almost any style that was not hoppy. I noticed if these beers were cold conditioned (bottles in the fridge for >4 weeks) that the head formation and retention got a lot better. Note: this was never a problem with hoppy American style beers, those alpha acids do wonders for foam formation and retention. I can't make any conclusions from this anecdotal evidence, but it may be something to try if you're having head retention problems.