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So as not to speculate, please provide the exact command you are using to su to the other account.
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1. login as user1 at box1
2. open a terminal window; in my case - Konsole
3. ssh box2
4. su user2
5. echo '/usr/local/bin/shellscript' | at hh:mm mm/dd/yyyy
As root, open the newly created at job script in /var/spool/atjobs. Notice the environment variables are from user1's environment, and not user2's environment.
1. login as user1 at box1
2. open a terminal window; in my case - Konsole
3. su user2
4. ssh box2
5. echo '/usr/local/bin/shellscript' | at hh:mm mm/dd/yyyy
As root, open the newly created at job script in /var/spool/atjobs. Notice the environment variables are from user2's environment --- as expected.