It is currently difficult to diagnose the situation where a cgi script fails to execute because permission bits have been set incorrectly. It would be very helpful if the cPanel error log provided a specific message when this situation occurs.
The error message you are referring to stems from Apache as opposed to cPanel. The cPanel interface is simply showing you what's output to the Apache error log for your account. You could consult with your hosting provider to determine if a change in the Apache log configuration is beneficial.