Get on a trainer, and spin for about 10 minutes. When you're comfortable, and in a bit of a groove, stop pedaling at bottom dead center, and have someone take a picture. Then measure your knee angle. It is possible to have your seat too high as well.
Check your cleat angle and position, the same for your seat as well. Any variance there could be the problem.
You say you're fairly new to riding on the road as well - 6 weeks - this could easily be an overuse symptom. Believe me, I know (2x knee surgeries since September). You need to knock back your volume, keep your cadence around 90ish and stick to flatter rides to avoid putting too much stress on your knees. Once you're feeling good for a couple weeks, and your position is good, you should be fine to begin ramping up your intensity.