I've been having this same problem (intermittent missing toolbars) for months on my primary system (Dell M4800, Windows 8.1 Pro), and just this past week I've seen it for the first time on a Surface Pro 2 (Win 8.1 Pro). On my M4800 it seems that if I wait a couple of minutes before logging into Windows (wait until the disk activity light quiets down which should indicate all services and such have started) then I usually do *NOT* have a problem and the toolbars are there. However, logging in as soon as possible seems more likely to lead to missing toolbars. When they aren't there, I wait until the Windows desktop is fully initialized and all expected System Tray icons are visible. Then I bring up the Task Manager, locate the Windows Explorer task and restart it. Instantly my (two - Quick Launch and a replacement Start menu) toolbars appear, and the rest of the Taskbar/System Tray also remains (actually redraws) unchanged.) I'd be curious to know if anyone else has observed (or can look for) a correlation between the disappearance of toolbars and how soon after system boot that you are signing in.
I know it doesn't make sense, but I have a weak working theory as to what might be going on, and an observation from the past that maybe related. First, the observation:
In prior versions of Windows (could be Win 7, could be Vista, could be XP - I'm not sure...) I've noticed a very infrequent behavior. I've always used the Quick Launch toolbar for my heavily used apps. Immediately after login it's not unusual for me to click on a Quick Launch icon. When I do this, usually the related application will load, albeit sooner or later - depending on the system I'm using and how snappy it is. However, what's interesting is that on rare occasion the application never loads. Sometimes I get impatient and click again, and then multiple instances load. But sometimes I'll click twice and wait, and still nothing loads! However, if I wait another minute or so (until the system seems to be less busy) then clicking on the same icon loads the related app immediately. This is what leads me to my working theory for those pesky missing toolbars:
I wonder if there are some desktop initialization actions which Windows Explorer handles that can time out "silently" - that is, without displaying an error? What I've described in the previous paragraph seems to be an example of this behavior. And perhaps the missing toolbars is another manifestation of the same issue?
Anyone have any thoughts on this?