mindgarden saidFor some reason, I've found that lifting barefoot (there is a foam mat under the squat cage) is better than squatting in shoes.
Potentially hazardous, but theoretically sound: lets you concentrate on maintaining the longitudinal arches of your feet (which, if compromised, leads to all kinds of BS within the knee joint).
Potentially hazardous? How? I mean if you drop 225lbs on your foot it's going to hurt no matter what.
Are you sure that you are activating your glutes and rotating out your femur? (pushes the knees apart)
Here's a Rippetoe page of squat help http://startingstrength.wikia.com/wiki/Squat_Videos
And you might want to have a look at Kelly Starrett's tips for mobilising for squatting http://www.mobilitywod.com/tag/squatting
And of course back off maybe 10-20% weight while you are trying out this stuff.