I suppose this issue my be related to my question 159345 (it is about
Natty). The cause of skipping .pam_environment some environment
variables may be in spaces within variable values. Looks like conffile
parser interprets quotes differently. Variables with quoted values
because of spaces got skipped with parse error.

You may check this with the following test. Please be careful.  If pam
configuration is broken, you may be not able to login.

In ~/.pam_environment add:

MYVAR0="SOME_VALUE"
MYVAR1="SOME VALUE"

In file /etc/pam.d/login find a line with pam_env.so and add there
option debug like follows:

session       required   pam_env.so debug readenv=1

Then login open a new console session and check results. In the session:

$ env | grep MYVAR
MYVAR0="SOME_VALUE"

only MYVAR0 is defined, but MYVAR1 is skipped. Also in /var/log/auth.log
you can see something like that:

May 31 11:02:39 host login[26761]: pam_env(login:session): Unrecognized
Option: VALUE"#012 - ignoring line

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https://bugs.launchpad.net/bugs/584249

Title:
  pam_env does not evaluate ~/.pam_environment

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