by Jukka Matikainen.
We have this issue as well, in an upgraded Moodle (2.2 -> 2.5) and in a fresh install. At first the files are shown correctly, but as soon as the treeview JavaScript is loaded, some of the files disappear. The files are not just hidden, they don't appear in the html source code at all.
The treeview works in all other pages, except the grading table. As a temporary fix we've disabled loading the treeview JavaScript by commenting out the line 59 in mod/assign/renderer.php
//$this->page->requires->js_init_call('M.mod_assign.init_tree', array(true, $this->htmlid));
Now the files are shown as html lists which is not as pretty but at least they are shown every time.