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    Not sure the answer, but it'll boil down to environmental. As a general point on problems like these, you might try to break it apart into separate pieces in the same temporary/test/one-time script, echo plenty of return codes and don't suppress any errors. For example, take the subshell commands, execute each individually then echo $? after each and then once again altogether as a subshell and echo $? that as well. Something will jump out at you. You can schedule that as a one time cronjob and examine the email generated. Commented Jun 7, 2013 at 12:22
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    Is it the same shell in both cases? Try this: ( set -o noclobber; echo $? > "$ecfile"; shopt > "$debugfile"; echo "$SHELL";) Commented Jun 7, 2013 at 14:20
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    Just explicitly force a shell through a shebang line ( #!/bin/bash ) or by using bash /your/path/and/file) Commented Jun 7, 2013 at 14:22
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    Post the full script. Also, add set -x at the top of the script just below the #! line, run the script from the command line, run the script from cron, and post both resulting traces. Commented Jun 7, 2013 at 22:30