Mostly because you are just starting out. Running is a high impact sport, so your extra weight does factor in as well. Your knees need time to adjust to the stress you are putting them under. Build up your distance gradually. Never run until your knees have recovered from your last running session. You might also have weak quadricep muscles which won't absorb as much of the shock of running transfering more impact to your knees. Developing leg strength through weight lifting can help a lot in improving your running and strengthening your knees. Lastly, make sure you are wearing a shoe designed for running. Orthotics can also help.
Should I just stick to the bicycle until I get my weight down. DAMN...I was really enjoying the running, but I don't know if it's just cause I am starting out, if it's bad form, or if it's cause I am too heavy.