It looks like you're trying to initialize the plugin while it doesn't exist on the DOM.
var templ = $('#slideTemplate').html();
var id = parseInt( $('ul.ui-sortable li').last().find('.order').val() ) || 0;
var slide = templ.replace(/%id%/g, id).replace(/%id1%/g, id + 1);
$('PARENT').append($(templ));
$(templ).find('.minicolors').minicolors();
Or if you want to work directly off the DOM:
var templ = $('#slideTemplate');
var id = parseInt( $('ul.ui-sortable li').last().find('.order').val() ) || 0;
var slide = templ.html().replace(/%id%/g, id).replace(/%id1%/g, id + 1);
templ.find('.minicolors').minicolors();