Looks like this is a dupe of 584249. There's a workaround in that one,
though I haven't tested it myself yet:

session required pam_env.so

Add that line at the end of /etc/pam.d/common-session is supposed to
force it to read the ~/.pam_environment afteram encrypted $HOME is
mounted.

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https://bugs.launchpad.net/bugs/952185

Title:
  ~/.pam_environment not parsed when HOME is encrypted

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