I have had a problem on a couple of chinense that no one has been able to identify. If you get close does it look anything like this?

Here is a link that might be useful: Leaf problem

Mdhuber,
I have had that same problem the last three years. I found that the plants would shed a lot of the affected leaves and then replace them, and did good after. I think the problem is related to over watering, at least in my case. When I cut way back on water and let the plant dry out to the point of almost wilting, the problem went away. This year it hasn't shown up, and I have been watching the water a lot closer.
Jim

Called edema, sometimes spelled oedema. An environmental thing that won't damage your peppers.

Yes...oedema! I seen this on our Poinsettia crops in the GH last year (school). Happens when roots take up more water than they can use in humid conditions :)
The cells in the leaves burst and cause the bumpy blister affect. Sometimes they can burst open if enviromental conditions are not corrected. It is more a cosmetic damage than anything.

Vera