Anyone else noticing menu that are attached to menu_minpanels disappearing on certain paths, e.g. /user?

The particular menu I'm trying to work with has five items, so I've added the following to menu_tree_check_access():

  if (count($tree) == 5) {
    kpr($tree);
    kpr(debug_backtrace());
  }

What I've noticed is that on some pages (homepage which is a node, /node, nodes of one particular content type) I get the above displayed once and in others (/user, nodes of another content type) I get two. In all cases, Furthermore on the two occasions the above is printed twice the second copies have different backtraces - on /user it goes through template_preprocess_page() while on one of the node pages it comes through shortcut_preprocess_page().