how do. just read this post with interest. im glad you've managed to get the issue investigated in more detail.
i had my acl repaired last june. uneventful rehab really but got flare ups and swelling when i exercised or stressed the knee a lot. also had painful and imited flexion. i gave it seven months of good rehab but was still happening. went in for a scope to sort the problem and my consultant found a soft tissue growth just anterior to the tibial insertion of my new acl. prob due to laydown of scar tissue/revascularising etc. my surgeon had never seen this before in near a thousand surgeries. whipped it out and not a bother since!
anyway. this doesnt sound a million miles from what your investigations have shown. hopefully its something that can be fixed quite easily also.
also, i could have been going for physio for years and it would have made no difference to this. sometimes a scope is the only option.