That is impressively complex for a "first perl program"!.

Others have directed you toward debugging (push a hashref into the array, instead of hash).

This note focuses more on perl STYLE - in particular, your use of c-style loops, which, although usable, are better written "perl style". Your loop:

for $i ( 1 .. $#allmolecules ) {
 ...
[download]

could be re-coded (untested) as:

for my $currentMolecule ( @allmolecules ) {
   ... 
   while (my ($key,$val) = each  %$currentMolecule ) { #line 222
                  if (ref($val) eq "ARRAY")
                  {     print "$key=@$val"; }
                  else
                  {    print "$key=$val"; }

     ...
   }
}
[download]

Note the use of "my" to localize the scope of temporary variables.
update: Changed inner "for" loop into a "while (my ($k,$v)=each.." loop after I noticed the O.P. needed both the key AND the value.