OK - I've got the same source as you, but still can't reproduce the problem.

Do you have 64-bit Windows, or 32-bit Windows ?
Is your compiler 64-bit or 32-bit ?

First thing is to concentrate on the contents of pod/perldelta.pod. Does line 5 of that file contain: 
perldelta - what is new for perl v5.16.3

[download]
It should. Specifically, for me that file begins with: 
=encoding utf8

=head1 NAME

perldelta - what is new for perl v5.16.3

=head1 DESCRIPTION

[download]
If that part's ok then we probably switch our attention to Porting/pod_lib.pl and insert some warn statements just prior to line 117 of that file - that will help us establish the reason that the failure occurs.

Cheers,
Rob

In reply to Re^5: Compile PERL from source on Windows by syphilis
in thread Compile PERL from source on Windows by MGoBlue

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