The first problem appears to be a bug in 5.6.1, already fixed in 5.8.0.

I think the second problem is just more of the first - I don't think 5.6.1 is handling the -F on the #! line correctly.

With 5.8.0, the #! version gives the same result as the command-line version.

Note that you don't seem to be allowed to separate the argument to -F into a separate argument:

  #!/usr/bin/perl -apnF "monkey"
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failed even under 5.8.0.

Hugo