This has been tested on RT 3.4.4 with scriptactulous.js already loaded in Header.

Replace EditCustomFieldSelect with the following, or see RT::Extension::CustomField::Checkbox

%# BEGIN BPS TAGGED BLOCK {{{
 %#
 %# COPYRIGHT:
 %#
 %# This software is Copyright (c) 1996-2005 Best Practical Solutions, LLC
 %#                                          <jesse@bestpractical.com>
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 %# (Except where explicitly superseded by other copyright notices)
 %#
 %#
 %# LICENSE:
 %#
 %# This work is made available to you under the terms of Version 2 of
 %# the GNU General Public License. A copy of that license should have
 %# been provided with this software, but in any event can be snarfed
 %# from www.gnu.org.
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 %# This work is distributed in the hope that it will be useful, but
 %# WITHOUT ANY WARRANTY; without even the implied warranty of
 %# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 %# General Public License for more details.
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 %# along with this program; if not, write to the Free Software
 %# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
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       <select name="<%$NamePrefix%><%$CustomField->Id%>-Values"
         size="<%$Rows%>"
         id="<%$id%>"
         <% $Multiple && 'MULTIPLE' %>>
 % my $selected;
 % my $CFVs = $CustomField->Values;
 % while ($CFVs and my $value = $CFVs->Next ) {
         <option value="<%$value->Name%>"
 % if ($Values) {
             <% $Values->HasEntry($value->Name) && ($selected = 1) && 'SELECTED' %>
 % } elsif ($Default) {
             <% ($Default eq $value->Name) && ($selected = 1) && 'SELECTED' %>
 % }
             ><% $value->Name%></option>
 % }
         <option value="" <% !$selected && 'SELECTED' %>><&|/l&>(no value)</&></option>
       </select>
 
 
 %if ($Checkboxes) {
 % # create a checkbox interface for the selection
 
   <script type="text/javascript">
 
   Element.hide('<%$id%>');
 
   $('<%$id%>').checbox_interface = Builder.node('div');
   $('<%$id%>').parentNode.insertBefore($('<%$id%>').checbox_interface, $('<%$id%>'));
   for (var idx in $('<%$id%>').options) {
 
     var option = $('<%$id%>').options[idx];
 
     if (option.value) {
       var new_checkbox = Builder.node('input',{type:'checkbox'});
 
       $('<%$id%>').checbox_interface.appendChild(Builder.node('div', {}, [
         new_checkbox,
         option.value
       ]));
 
       new_checkbox.selected = option.selected;
 
       Event.observe(new_checkbox, 'click', function(event) {
 
         if (this.selected) {
           this.selected = false;
         }
         else {
           this.selected = true;
         }
 
       }.bindAsEventListener(option));
     }
     else {
 
       option.selected = false;
     }
   }
 
   </script>
 
 % }
 
 
 <%INIT>
 my $id = $NamePrefix . $CustomField->Id;
 </%INIT>
 <%ARGS>
 $Object => undef
 $CustomField => undef
 $NamePrefix => undef
 $Default => undef
 $Values => undef
 $Multiple => 0
 $Checkboxes => undef
 $Cols
 $Rows
 </%ARGS>