Looks like I failed to understand exactly what was happening here

builds/4chan-X.user.js

@@ -1744,14 +1744,14 @@
     setBoardList: function() {
       var a, boardList, btn, fourchannav, fullBoardList;
       fourchannav = $.id('boardNavDesktop');
-      if (a = $("a[href*='/" + g.BOARD + "/']", fourchannav)) {
-        a.className = 'current';
-        $.on(a, 'click', Index.cb.link);
-      }
       boardList = $.el('span', {
         id: 'board-list',
         innerHTML: "<span id=custom-board-list></span><span id=full-board-list hidden><span class='hide-board-list-container brackets-wrap'><a href=javascript:; class='hide-board-list-button'>&nbsp;-&nbsp;</a></span> " + fourchannav.innerHTML + "</span>"
       });
+      if (a = $("a[href*='/" + g.BOARD + "/']", boardList)) {
+        a.className = 'current';
+        $.on(a, 'click', Index.cb.link);
+      }
       fullBoardList = $('#full-board-list', boardList);
       btn = $('.hide-board-list-button', fullBoardList);
       $.on(btn, 'click', Header.toggleBoardList);
@@ -1772,7 +1772,7 @@
       }
       as = $$('#full-board-list a[title]', Header.bar);
       nodes = text.match(/[\w@]+((-(all|title|replace|full|index|catalog|url:"[^"]+[^"]"|text:"[^"]+")|\,"[^"]+[^"]"))*|[^\w@]+/g).map(function(t) {
-        var a, board, m, _i, _len;
+        var a, board, current, m, _i, _len;
         if (/^[^\w@]/.test(t)) {
           return $.tn(t);
         }
@@ -1798,7 +1798,11 @@
           a = as[_i];
           if (a.textContent === board) {
             a = a.cloneNode(true);
-            a.textContent = /-title/.test(t) || /-replace/.test(t) && $.hasClass(a, 'current') ? a.title : /-full/.test(t) ? "/" + board + "/ - " + a.title : (m = t.match(/-text:"(.+)"/)) ? m[1] : a.textContent;
+            current = $.hasClass(a, 'current');
+            if (current) {
+              $.on(a, 'click', Index.cb.link);
+            }
+            a.textContent = /-title/.test(t) || /-replace/.test(t) && current ? a.title : /-full/.test(t) ? "/" + board + "/ - " + a.title : (m = t.match(/-text:"(.+)"/)) ? m[1] : a.textContent;
             if (m = t.match(/-(index|catalog)/)) {
               a.dataset.only = m[1];
               a.href = "//boards.4chan.org/" + board + "/";

builds/crx/script.js

@@ -1754,14 +1754,14 @@
     setBoardList: function() {
       var a, boardList, btn, fourchannav, fullBoardList;
       fourchannav = $.id('boardNavDesktop');
-      if (a = $("a[href*='/" + g.BOARD + "/']", fourchannav)) {
-        a.className = 'current';
-        $.on(a, 'click', Index.cb.link);
-      }
       boardList = $.el('span', {
         id: 'board-list',
         innerHTML: "<span id=custom-board-list></span><span id=full-board-list hidden><span class='hide-board-list-container brackets-wrap'><a href=javascript:; class='hide-board-list-button'>&nbsp;-&nbsp;</a></span> " + fourchannav.innerHTML + "</span>"
       });
+      if (a = $("a[href*='/" + g.BOARD + "/']", boardList)) {
+        a.className = 'current';
+        $.on(a, 'click', Index.cb.link);
+      }
       fullBoardList = $('#full-board-list', boardList);
       btn = $('.hide-board-list-button', fullBoardList);
       $.on(btn, 'click', Header.toggleBoardList);
@@ -1782,7 +1782,7 @@
       }
       as = $$('#full-board-list a[title]', Header.bar);
       nodes = text.match(/[\w@]+((-(all|title|replace|full|index|catalog|url:"[^"]+[^"]"|text:"[^"]+")|\,"[^"]+[^"]"))*|[^\w@]+/g).map(function(t) {
-        var a, board, m, _i, _len;
+        var a, board, current, m, _i, _len;
         if (/^[^\w@]/.test(t)) {
           return $.tn(t);
         }
@@ -1808,7 +1808,11 @@
           a = as[_i];
           if (a.textContent === board) {
             a = a.cloneNode(true);
-            a.textContent = /-title/.test(t) || /-replace/.test(t) && $.hasClass(a, 'current') ? a.title : /-full/.test(t) ? "/" + board + "/ - " + a.title : (m = t.match(/-text:"(.+)"/)) ? m[1] : a.textContent;
+            current = $.hasClass(a, 'current');
+            if (current) {
+              $.on(a, 'click', Index.cb.link);
+            }
+            a.textContent = /-title/.test(t) || /-replace/.test(t) && current ? a.title : /-full/.test(t) ? "/" + board + "/ - " + a.title : (m = t.match(/-text:"(.+)"/)) ? m[1] : a.textContent;
             if (m = t.match(/-(index|catalog)/)) {
               a.dataset.only = m[1];
               a.href = "//boards.4chan.org/" + board + "/";

src/General/Header.coffee

@@ -135,12 +135,12 @@ Header =
 
   setBoardList: ->
     fourchannav = $.id 'boardNavDesktop'
-    if a = $ "a[href*='/#{g.BOARD}/']", fourchannav
-      a.className = 'current'
-      $.on a, 'click', Index.cb.link
     boardList = $.el 'span',
       id: 'board-list'
       innerHTML: "<span id=custom-board-list></span><span id=full-board-list hidden><span class='hide-board-list-container brackets-wrap'><a href=javascript:; class='hide-board-list-button'>&nbsp;-&nbsp;</a></span> #{fourchannav.innerHTML}</span>"
+    if a = $ "a[href*='/#{g.BOARD}/']", boardList
+      a.className = 'current'
+      $.on a, 'click', Index.cb.link
     fullBoardList = $ '#full-board-list', boardList
     btn = $ '.hide-board-list-button', fullBoardList
     $.on btn, 'click', Header.toggleBoardList
@@ -184,7 +184,11 @@ Header =
         if a.textContent is board
           a = a.cloneNode true
 
-          a.textContent = if /-title/.test(t) or /-replace/.test(t) and $.hasClass a, 'current'
+          current = $.hasClass a, 'current'
+          if current
+            $.on a, 'click', Index.cb.link
+
+          a.textContent = if /-title/.test(t) or /-replace/.test(t) and current
             a.title
           else if /-full/.test t
             "/#{board}/ - #{a.title}"