Could you be Suffering from Buffering for the log file? Could you have the network device syslog the commands being executed instead of trying to rely on logging them in your script instead?
FWIW, here's what I used to do in 7+ year old script:
print $expect_instance "show system\r";
( $which, $why, $match, $before, $after ) = $expect_instance->expect(
+$Timeout, '#');
if( ! $which ) { mylog( $dev, 'sho_sys', $why ); return; }
$sho_sys = $before;
Not familiar with the sub method you are using, but the last time I used Perl Expect was several years ago. :(
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