There are obviously a number of ways to improve the code

You probably don't want to be using variable variable names (which makes your root problem go away).. A bunch of nodes, including the following two, refer to the reasons:
Have to also throw out the obligatory comment about avoiding the use of $a and $b because of their special global-ness w/sort

Could you also provide sample input & output to this sub? I strongly suspect this could be written w/ map & join .. something like (note the hash slice usage): 
sub meld_columns {
  my ($arrays, @arrNames) = @_;
  my ($maxIdx) = sort { $b<=>$a } map {$#$_} @{$arrays}{@arrNames};
  my @outarray = map {
    my $i = $_;  # keep track of the current "row" to use in inner map
+ block
    # get the respective element from each array.
    # If we're beyond the individual array length, just use "\t".
    # Also glue all cols together w/a "\t"
    join "\t", map { $i <= $#$_ ? $_->[$i] : "\t" } @{$arrays}{@arrNam
+es}
  } 0..$maxIdx;
}
my %arrayHolder = map { $_ => [] } 'a' .. 'z';   # build the initial d
+ata structure (instead of named arrays)
my @out = meld_columns( \%arrayHolder, 'a' .. 'h' );  # meld just A th
+rough H
my @out = meld_columns( \%arrayHolder, 'f', 'a', 'c' );  # meld just F
+ A C, in that order.

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In reply to Re: my vs. local subtlety by davidrw
in thread my vs. local subtlety by esr

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