I encountered similar problem. And using the knowledge from Etoile i changed the shortcodes file in mentioned lines as :
Every line mentioned commented and added new one as :
$CategoriesString .= "<a href=\"?categories=" . $Category->Category_ID . "\">";
Additionally commenting the line
//if (in_array($Category->Category_ID, $category)) {$CategoriesString .= "checked=checked";}
and deleting the “>” sign in the next line.
For example my line 1380 looks like that:
//$CategoriesString .= "<input type='checkbox' name='Category" . $Category->Category_ID . "' value='" . $Category->Category_ID . "' onclick='UPCP_DisplayPage(\"1\"); UPCPHighlight(this, \"" . $Color . "\");' id='cat-". $Category->Category_ID ."' class='jquery-prod-cat-value'";
$CategoriesString .= "<a href=\"?categories=" . $Category->Category_ID . "\">";
//if (in_array($Category->Category_ID, $category)) {$CategoriesString .= "checked=checked";}
$CategoriesString .= "<label class='upcp-label' for='cat-". $Category->Category_ID ."'> <span>" . $Category->Category_Name . " (" . $ProdCats[$Category->Category_ID] . ")</span>" ;