If the pain kicks in just above parallel, and worsens with increased depth you might have bursitis. No amount of strengthening will help. It's the motion that's aggravating the injury, and so it's the motion that needs to be restricted. One option that helped for me was tightening up my squat stance width, which helped dramatically. I also got got some coaching on my squat form for other reasons, but it also helped take a little bit of the pressure off.
It did. When the injury didn't go away, I did some searching around this site and saw some others who noted that they had narrowed their stance. I made small repetitive adjustments until I got to a place where I could squat without pain. I had to drop some weight on the bar (about 15%) and build up comfort in in the position. It beats not squatting for three months.