I'd expect it to be worse going downstairs, though, if it were a saddle height/kneecap tracking thing.
I've had mine take longer than that to resolve, a couple of times. Are your knees swollen? A little puffy between the kneecap and the tibia?
The good news about "chondromalacia" aka patellofemoral syndrome is that with good knee alignment on your bike (seat height for sure, but also cleat alignment and crankarm length) and some guidance on strengthening the right muscles, you should be fine. The ortho won't want to know you since it's totally non-surgical - get a referral for PT, find a good one, get a good bike fit, heal up quick.
