config.macros.anchorjumpを差し替えて、clickイベントの処理を修正。scrollAnchorVisibleは手を入れたのでこの中に取り込みました。

config.macros.anchorjump = {
handler: function(place,macroName,params,wikifier,paramString,tiddler){
if(!params[0] || params[0] == "") return;
if(!params[1] || params[1] == "") return;
var anchor = params[0];
var title = params[1];
var e = createTiddlyElement(place,"span");
e.innerHTML = "<html><a name='anchorjump' href=\"javascript:;\" onclick=\"config.macros.anchorjump.scrollAnchorVisible('"+anchor+"', event);\">"+title+"</a></html>";
},
scrollAnchorVisible: function(anchorName, evt) {
var target = resolveTarget(evt);
var tiddlerElem = story.findContainingTiddler(target);
var ispopup = false;
if (!tiddlerElem) {
tiddlerElem = jQuery("#popup").get(0);
ispopup = true;
}
if (!tiddlerElem) return;

var children = tiddlerElem.getElementsByTagName('a');
for (var i = 0; i < children.length; i++) {
var child = children[i];