I have the same problem in Debian 9 Stretch, net.netfilter.nf_conntrack_max and 
net.nf_conntrack_max does not apply after reboot. The pure solution is load 
module nf_conntrack before sysctl. You can do this with the command:
echo "nf_conntrack" >> /etc/modules

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https://bugs.launchpad.net/bugs/50093

Title:
  Some sysctls are ignored on boot

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