Actually many have found full range squats very theraputic for knee issues. These same people have reported problems tolerating 1/2 and parallel squats.
I just posted in this old thread last night. It has a few people stating as much. If you scroll down to my post, #20, you'll find research and references for exactly why this is (and it's not like it isn't well known, there's just the old wives tale - full squats are natural to the body appropriately load knees, hips, hams, glutes rather than placing sheer directly on the knee during reversal at parallel.
http://www.fortifiediron.net/invisio...howtopic=11759
I will note that some people will try to switch to full range squats and use too heavy a weight right away (i.e. they are used to partial movements or machines) and this might cause some aggrivation and issues but if you build at a reasonable pace most find these to be a godsend for knee issues. They certainly were for me.