By reducing your subroutine to the bare essentials, we appear to get the following (with some variable name munging to make it easier to read):

my ($initial_enthalpy, $initial_entropy) 
    = get_initials ($terminal[0], $initial_enths[1], $initial_entros[1
+]);

sub get_initials {
  my ($terminal, $enths, $entros) = @_;

  my ($initial_entropy, $initial_enthalpy);
  if ( $terminal =~ /^[GC]/) )    {
    return ($enths, $entros);
  }
}
[download]

Which is the same as:

my ($initial_enthalpy, $initial_entropy) = $terminal[0] =~ /^[GC]/
    ? ($initial_enths[1], $initial_entros[1])
    : (undef undef);
[download]

From what I see, your += assignments in the subroutine suggest that you expect these variables to be incremented, even though their initial scope is in this subroutine and thus will be equivalent to zero wheen incrementing. Perhaps if you tell us what you're trying to do (and show us sample inputs and outputs), we can clear this up for you.

Cheers,
Ovid

New address of my CGI Course.
Silence is Evil (feel free to copy and distribute widely - note copyright text)