I recently had something similar with a presta valve.

Tire went flat, couldn't find a leak, so I just replaced it. Being an engineer, I wanted to find the source of the leak, though, so it wasn't until I submerged the stem that I saw air coming out the top of the valve. Not a lot of air, but enough that it would deflate after about 3 hours.

I took the valve out completely, cleaned it, and re-installed it, and it seems to be hold air again. I'm not sure what caused it, but it could be anything.