Just wondering, as this appears to be something with what is printed from uptime.pl, what is uptime.pl doing, and when this works from the command line, are you running as the same user as the CGI would run ?
My guess is that uptime.pl is doing something not allowed by the user (usually nobody). Usually, if works ok on the command line, but not in CGI it is the diffrence in user access or environment ... so i ould check if uptime.pl uses any of %ENV or external command.

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OH, a sarcasm detector, that’s really useful