1) Don't bootstrap the ACL. If you don't need the ACL for your shell-bound php script, then skipping that ought to ensure that none of those weird SQL clauses show up.
2) Try something like this in your script:
// Decide which user to authenticate
$user = $db->getTable('User')->find($id);
Omeka_Context::getInstance()->currentuser = $user;
// Now do everything else.
Kris
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