I had atrphy of my left leg when i had a sydrome with my glutes ( were tight and pulling the muschles down my leg and kee out of alignment causing pain), which was mis diagnosed as a anterior-cruciate ligament ( gotta love the toatly wrong diagnosis) . anyhoo, after 3 months in a kneebrace staying off the leg i had lost somthing like 2 cm of muscle on my thighs. this has almost all come back now after a couple of months on the bike
in short, if in doubt see a knee especialist. if your in sydney i can recomend you to a great one. at least see a physio.