Yeah, definitely take time off. You say the pain is behind your kneecap. Is it directly behind the kneecap? If so, then it could be chondromalacia (with damage that is not easily reversible). But I would make sure it's not a muscle or tendon issue first. I would agree with experimenting some more with raising seat height, even if you've already been fitted, just to see if the pain goes away.

Be careful with the ibuprofen though! Make sure that when you attempt riding your bike again that you haven't taken ibuprofen in the past day. Why? Because it can mask pain -- and pain is a sign that something is wrong. I "ibuprofen-masked" my running injury and continued running on it because without pain I didn't realize there was a problem.