Interesting. I found in the Perl script, if I print a string to the LCD prior to calling lcd_char_def() it works. So I took a step back and in the actual function itself, I added a call to lcdPuts(), and printing a newline (which is essentially a zero-width char on the display). This fixes it.

sub lcd_char_def {
    shift if @_ == 4;
    my ($fd, $index, $data) = @_;
    lcdPuts($fd, "\n");
    my $unsigned_char = pack "C[8]", @$data;
    lcdCharDef($fd, $index, $unsigned_char);
}
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So I have a code problem somewhere it seems, but at least this is a cheesy workaround until I can track it down.