Well in tortoise's case, I agree it's a custom draw issue given the entry IS there, yet it's really small and has no text nor icons displayed. The entries are still functional, and you can get a tooltip showing the description when you let your mouse cursor on the empty line.
For awxDTools, the submenu entry isn't there at all.
After giving it some thoughts, I believe it started to happen after I added some custom folders (smart favorites, recent locations, etc) to the default menu for files & folders using this method.
Of course removing those folders do not change the problem. I might try to reinstall DO.