So the setgid bit which causes this effect is actually on purpose; from
README.Debian:
Setgid ssh-agent and environment variables
------------------------------------------
As of version 1:3.5p1-1, ssh-agent is installed setgid to prevent ptrace()
attacks retrieving private key material. This has the side-effect of causing
glibc to remove certain environment variables which might have security
implications for set-id programs, including LD_PRELOAD, LD_LIBRARY_PATH, and
TMPDIR.
If you need to set any of these environment variables, you will need to do
so in the program exec()ed by ssh-agent. This may involve creating a small
wrapper script.
** Changed in: openssh (Ubuntu)
Status: Confirmed => Won't Fix
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LD_LIBRARY_PATH set in ~/.profile doesn't stick
https://bugs.launchpad.net/bugs/315591
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