Digging around a bit I wonder if this is the issue:

https://bugs.launchpad.net/ubuntu/+source/xorg/+bug/380360

So when you login, .profile is sourced. Then everything is parented to
ssh-agent (I assume to inherit the environment variables that it sets)
but as that is setuid, LD_LIBRARY_PATH is reset for security reasons.

However the usecase for wanting a per-user (i.e. not system wide) local
prefix for development libraries is pretty valid. I don't want other
users on the machine to be picking up my libraries when they run stuff,
but I do want the setting to be session wide so it is picked up by
applications I load from the command line.

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LD_LIBRARY_PATH not loading from .profile nor /etc/environment
https://bugs.launchpad.net/bugs/366728
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