With ligament tears, arthritis is common. Your Milly could already have some arthritis, hence her being stiff when she gets up. My Izzy tore her acl in her right knee when she was only 18 months, and then the left after her 2nd birthday (she is now 2.5yrs old). She has arthritis in both knees. They said the longer you wait to get the surgery, the worse the arthritis can get, and I had Izzy's done right when I found out what it was. I also feel that the glucosamine/chondrotin/MSM works great! I ran out of it, and forgot to give Izzy more. We went to physical therapy the other day and she was very stiff. She also was having trouble doing the water treadmill, even though she did great the week before. I then remembered that I forgot to start her back on the glucosamine. I put her back on, and her knee is less stiff. We are still working on her physical therapy and hopefully she will be back to normal soon. She is 4 month post-op from her most recent surgery.
I hope you find out what is going on with Milly soon. It sounds like an acl tear just from what you have said. It seems very common in boxers. Izzy's orthopedic surgeon said that she sees a lot of boxers, more than any other breed.
Please keep us posted on Milly.