> the help switch that is getting mixed in with them that appears in random order.

Your examples show -h not at a random position but either on the first or last position, this seems sensible for a generated switch.

What happens if you include -h in your fixed list?

The -h also sometimes appears mixed with the other options:

creates commands for a dzil profile minted with "cli"
    -d STR --dir STR           directory where distribution is located
    -c STR --cmd STR           command name
    -h -? --usage --help       Prints this usage information.
    -s STR... --subcmd STR...  subcommands to create
[download]

If I switch one of the options to -h as well, I get this:

creates commands for a dzil profile minted with "cli"
    -h STR --dir STR           directory where distribution is located
    -c STR --cmd STR           command name
    -h -? --usage --help       Prints this usage information.
    -s STR... --subcmd STR...  subcommands to create
[download]

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File a bug?

I think you should talk to the author.

Cheers Rolf
_{(addicted to the Perl Programming Language and ☆☆☆☆ :)
Wikisyntax for the Monastery}