RQ99,
Squats place an extreme amount of pressure on the back side of the patella. The vector forces when doing squats, puts almost all of the stress directly back against the femur. They are usually not recommended in anyone with a knee problem, and no one should ever go past ninety degrees.
Retropatellar pain is common in almost all ACL reconstructions, but more so is ones that use a B-T-B graft. Though the patellar cartilage is not violated in taking the graft, for some reason, retropatellar pain is common.
If the graft was loose, or if you tore the graft, you would have symptoms of laxity. The knee would shift in the anterior-posterior direction. It doesn't sound like you have that problem. When you see your PT you can have him/her check the knee for stability.
Retropatellar pain is very common in the human population, not just in people who have had their ACL's reconstructed. So, it is something that you will probably have to learn to deal with throughout your life.
Tell your PT so he/she can develop a strengthening program that doesn't involve so many squats.
Keep up the good work, it takes a concerted effort to get back after a significant injury. But, you have a goal to work for. Good luck.