I think that just happens sometimes. My sister once broke her toe (her PE teacher rolled a trampoline over it!) and it clicks all the time. I've injured my ankles (sprains from sport) and even after resting them, I occasionally get a large amount of pain that only goes away when I pop it or click it.
It could also be, as you said, due to underuse. It's trapped gas that generally is the problem that would ordinarily be dispersed during exercise.
If it does become problematic, perhaps try cod-liver oil. It's really good for your joints. Also, my mum has arthritis and finds glucosamine really helps. Although, apprently in the US it isn't sanctioned for human use. On the off chance you're not American... check it out. http://en.wikipedia.org/wiki/Glucosamine