Gli accapo "\n" che per il codice html sono solo un di più per js sono rilevanti, per cui così funziona:

codice:
#!c:/Perl/bin/Perl.exe
#
use strict;
use DBI qw(:sql_types);
use CGI ':standard';
use POSIX;
my $version = 'ITALIA';
my $max_records = 10;
# NO Buffer dell' output
select STDOUT;
$| = 0;
#

print ( "Content-type: text/html\n\n" );
print ( "<HTML>\n ");
print ( "<head>\n");
print ( "<script language=\"javascript\">\n");
print ( "<!--\n\n");
print ( "function CheckboxSeleziona_onclick() {\n");
print ( "var ck = document.getElementById(\"table3\").getElementsByTagName(\"INPUT\");\n");
print ( "for(var i = 0; i < 20; i++)\n");
print ( "if(ck[i].type == \"checkbox\") ck[i].checked = true;\n");
print ( "}\n\n");
print ( "//-->\n");
print ( "</script>\n");
print ( "</head><body>\n"); 

print ( "<TABLE BORDER=1 CELLPADDING=4 CELLSPACING=0 WIDTH=100\% BGCOLOR=\"#FFFFFF\" ALIGN=\"CENTER\">\n");
print ("<TR>\n<td align =\"center\"><input type=\"button\" value=\"SELECT ALL\" onClick=\"return CheckboxSeleziona_onclick()\"></td>\n");
print ("<td align =\"center\"><input type=\"button\" value=\"DESELECT ALL\" onClick=\"return CheckboxDeSeleziona_onclick()\"/></td>\n</tr>\n</TABLE>\n");
print ( "<TABLE BORDER=1 CELLPADDING=4 CELLSPACING=0 WIDTH=100\% BGCOLOR=\"#FFFFFF\" ALIGN=\"CENTER\">\n");
print ("<TR><td align =\"center\"><input type=\"button\" value=\" MO \" onClick=\"java-script:history.back()\"></td>\n");
print ("<td align =\"center\"><input type=\"button\" value=\" MT \" onClick=\"java-script:history.back()\"></td></tr></TABLE>\n");
print ( "<TABLE id=\"table3\" BORDER=1 CELLPADDING=4 CELLSPACING=0 WIDTH=100\% BGCOLOR=\"#FFFFFF\" ALIGN=\"CENTER\">\n");

print ("<TR\n><TD><input type=\"checkbox\" name=\"form_mi18\" value=MI18> MI 18</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_bo12\" value=BO12> BO 12</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_rm15\" value=RM15> RM 15</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_na08\" value=NA08> NA 08</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_mi22\" value=MI22> MI 22</TD>\n</TR>\n");

print ("<TR>\n<TD><input type=\"checkbox\" name=\"form_mi19\" value=MI19> MI 19</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_bo13\" value=BO13> BO 13</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_rm16\" value=RM16> RM 16</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_na09\" value=NA09> NA 09</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_bo16\" value=BO16> BO 16</TD>\n</TR>\n");

print ("<TR>\n<TD><input type=\"checkbox\" name=\"form_mi20\" value=MI20> MI 20</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_bo14\" value=BO14> BO 14</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_rm17\" value=RM17> RM 17</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_na10\" value=NA10> NA 10</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_rm19\" value=RM19> RM 19</TD>\n</TR>\n");

print ("<TR>\n<TD><input type=\"checkbox\" name=\"form_mi21\" value=MI21> MI 21</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_bo15\" value=BO15> BO 15</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_rm18\" value=RM18> RM 18</TD>\n");
print ("<TD><input type=\"checkbox\" name=\"form_na11\" value=NA11> NA 11</TD>\n");
#print ("<TD><input type=\"checkbox\" name=\"form_rm20\" value=RM20> RM 20</TD>");
print ("<TD><input type=\"checkbox\" name=\"form_na14\" value=NA14> NA 14</TD>\n</TR>\n");
print ( "</TABLE></BODY></HTML>\n");