Hiho,
I just tried to reproduce your problem and everything worked fine! I am not too good with perl regexps but I changed only things which connot have any relation with your problem. Here is some modified code:

#!/usr/bin/perl -w
#A program that accept an input file: Scorpion database from Gen Bank
#and will output the database in BioWare format

my $file1="$ARGV[0]";        #var to save the input database
my $counter=1;

open(INFO1,$file1) or die "Can't open $file1.\n";#open file1
foreach(<INFO1>)
{
    if(/DATE\s*(.*)-(.*)-(.*)/){
    print 'DATE'."\t".'"'."$1-$2-$3".'"'."\n";
    }                                             
    elsif(/\s*\/intron=(.+)\n/) {
    my $item;
    my $local=$1;
    $local =~ s/\"//g;
    foreach $item (split('\;',$local)) {
        $item = " - " if $item =~ " ";
            print "Intron\t \{Translation%$item\}\n";
    }
    } #end elsif
    
    elsif(/\s*\/exon=(.+)\n/) {
    my $item;
    my $local=$1;
    $local =~ s/\"//g;
    foreach $item (split('\;',$local)) {
        $item = " - " if $item =~ " ";
        print "Exon\t", " \{Translation\%","$item\}","\n";
    }
    }
}
[download]

The significant changes are

• Added a semicolon after  my $file1="$ARGV[0]"
  
• Removed the circonflex in   if(/^DATE\s*(.*)-(.*)-(.*)/)
  
• Added the if-statement to handle empty transaction-strings

Now I get the following output with your example

michael@trul:~/> perl prog.pl input
DATE    "13-JUN-2000"
Exon     {Translation%49-333}
Intron   {Translation%1-48}
Intron   {Translation%334-385}
DATE    "14-JUN-2000"
Exon     {Translation%1-120}
Intron   {Translation% - }
[download]

So in my opinion everything works as desired.

Regards