...and how to fix them.
When running a Perl CGI script, you may see the "premature end of script headers" error in your Apache error.log or error_log file. This can be caused by some of the same problems (and fixed with some of the same fixes) as the Internal Server Error message. However, this can also be caused by suEXEC errors, and in that case, it may give you no indication whatsoever that suEXEC is the cause.
Check if you have a /var/log/apache/suexec.log file; if so, and if it's the problem, it'll explain the reason why it's denying your script from executing properly. One easy fix to try is adding a "-w" to the end of the first line of your Perl script, i.e. change the first line from "#!/usr/bin/perl" to "#!/usr/bin/perl -w" and see if that makes suEXEC happy. Another common fix is to make sure that your CGI script has the same user/group ownership as your cgi-bin folder.