Since gpg-agent is being run through the $STARTUP chain, sourcing that
$PID_FILE seems unnecessary if gpg-agent gets actually invoked by this
script. If I get things correctly, this sourcing part of the script is
only intended to recover access to a (leftover?) gpg-agent that is
already running when this script is entered.

Maybe your problem is related to this one instead:
https://bugs.launchpad.net/ubuntu/+source/gnupg2/+bug/743268

I applied that patch given there and everything works fine.

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https://bugs.launchpad.net/bugs/804641

Title:
  gpg-agent incorrectly detects currently running daemons

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