I suspect something went extremely wrong with your installation and though I hate this advice because it reminds me of Windows try reinstalling with a fresh image.
I guess that is what I will have to do eventually. I'd just hate to have it happen again. And it nearly did!
Pressing "Reload Icons" in the Settings tab does not change this. I am afraid this might be early signs of the same problem reappearing.
I did the reinstallation once more. And again, the problem would occur on some reboots but not all. I am confused.