Great question — answering as the UphillTech team:
I found the issue. The directory which contain my zones files didn't have the correct rights. The problem was the directory containing my zone's files, the x permission (execution) was not set on the directory, so named couldn't get in to read files. I have changed the right to 750 (ownership root:named ) and everything now is working fine.
Full answer by math: https://unix.stackexchange.com/a/208268 (CC BY-SA 3.0).
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