Chondromalacia patella generally presents with a lot of pain, both dull and sharp, at just about all times (I know because I have the stupid thing). In your case, it could just be popping joints, particularly if you aren't experiencing and pain during or post workouts.
Could be genetic, form-related, wear and tear related. A trip to the doc *may* help you get to the bottom of this, then again, it may not, even with some expensive MRI/xrays.
As pain is not a factor, and you seem to present no signs of weakness or instability, you may simply have joints that crack, not unlike someone's fingers. I'd just keep a really close eye on it, and have someone you know and trust (ie. exercise professional) critique your form for the time being, and if you start experiencing pain, weakness, or instability either during or in between workouts, get to your doc.