Some questions:
- Are you using ice or heat on your knee?
- If not, try one or both. Do they help?
- As the weight has gotten heavier on the bar, are your knees sliding forward at the bottom of the squat?
- At the bottom of the squat, do you shoot the hips back and open the knee angle forcing more of a good morning motion on the squat?
I'm not a doctor and you were pretty vague about where your pain is occurring. However, it's probably best to start simple. This sounds a lot like patellar tendonitis, or tendonosis. Resting a bit might be initially useful, but as you have seen, it will just come back anyway. You probably need to find a way to manage the pain and train around/through it. I have had patellar tendonitis on and off. I no longer suffer from it. The solution? Gain weight, get stronger, and squat with good form. You may not have tendonitis, in which case the above advice may not apply.