You inadvertently stumbled on to the solution by installing stretch, since the fix is in dnsmasq 2.76.
The actual problem is detailed below, along with a fix for jessie.
The solution I first discovered here:
https://www.raspberrypi.org/forums/viewtopic.php?t=128449#p919942
Then found the bug ticket here:
The diff patch to fix is here:
https://bugs.debian.org/cgi-bin/bugreport.cgi?att=3;bug=858506;filename=dnsmasq-init.patch;msg=27
You can install a more recent version of DNSMASQ here:
Update: 2018-08-06
As of v4.0, Pi-hole ships with _FTL_DNS, our fork of dnsmasq, which should restore compatibility with Raspbian Jessie. We still recommend installing a newer OS as Jessie is EOL anyway.
Please note that this tutorial is only meant for Rasbian Jessie, although it might (to some extend) also help with similar issues on other Debian versions. Do this at your own risk (however, the likeliness of a failure is rather small in our opinion).
First step: Download more recent versio…
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