Well, you will get this error message if the shebang line is actually no more used as such:

$ cat example
#!/usr/bin/perl -T
print "hello\n";
$ chmod u+x example; example
hello
$ perl example
Too late for "-T" option at ol line 1.
[download]

I can only guess what this means: When you start a script with `perl scriptname`, perl starts up and might enable the "taint mode" or not and _then_ takes your script. Because it's clever it examines the input file for a shebang line and tries to get as much as possible out of it, but '-T' can no more be evaluated. If you start your script as `scriptname`, the shebang is _really_ the perl-call and so perl gets all startup-information from that line. In CGI environment the shebang is also the startup-information-source for perl, so it's not "too" late there.

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