My only problem with the Humble library is that it takes eons for the game updates to become available, and when they are, you have to download the whole game again, there's no separate patch. Which kind of sucks when it's a, let's say, 6 GB download.
But I never had the problem you mention, every time I bought a game from the Humble Store or I received a gift key for a game purchased there, it was instantly added to my library (except pre-orders). I remember there was some delay with the DRM-free version of Ether One when it was released, but I don't know if it was the developer's fault or Humble's.