Title problems do come up. With all the selling of mortgages and mortgage backed securities title can become confused. Possibly there is a third party involved and HUD was not aware of it.
They will get it straightened out. Just remember that it is not the title company's fault. Keep in regular contact but not so much that you are a bother. And an occasional thank you is always welcome.
You need to check with the title company to see what's holding things up, and you need to be thankful that the title company is doing its job to protect you. It's entirely possible that there are environmental liens, tax liens, various mechanics liens, or other liens that need to be cleared. It's also possible that the chain of title isn't clean, and needs to be fix before that--or any other--title company can issue a full warranty deed. Otherwise, you might not be able to sell this property free and clear later on.