One problem is that the government really doesn't know who owns what. They don't have the library/IT infrastructure to manage all of that knowledge and some of them don't evem care.
I don't live in Africa and haven't read enough about it, so assume that a lot of this post is conjecture. I'm trying to base this off of Hernando deSoto's "The Mystery of Capitalism", but I can't remember enough of it and I'm probably mangling the message horribly. He did a lot of research on property rights in various countries, and is apparently working with the Peruvian government to change the way their legal system deals with the issue.
If you're going to make improvements in a town's infrastructure, you need to know who's paying for it, which would be the people living there: if you don't know who they are (and can't tax them) you might be much less likely to make such improvements. If they do know who owns the land, it's usually obsolete or uninformative, because whoever did own the land might have sold it to someone
What they need to do is map out who lives where and say that; "okay: if you have lived here for five years or so and you have made improvements to it (think of America's Homestead Act), you will be marked down as owning this land and you will be given a deed to it. You can sell this house and your land to whoever you want (and we will make it easy for you to record that on our servers*.)."
*In most places, you have to go through such a ludicrous number of bureaucratic steps to transfer the deed to your property that people don't even bother informing the government that someone else now owns it.
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