Looking through the book, I didn't see much if anything that really seemed overpowered. Plus, the editing is much better than the editing in Swashbuckling Adventures, which makes me predisposed to like the book.
There are a couple of areas where a WOTC product would have spelled things out more clearly I think, though, such as the description of the African Cleric class which doesn't mention the ability to spontaneously channel cure spells. I think a WOTC product would've mentioned specifically that the African Cleric can't channel cures, whereas the Nyambe book just doesn't mention anything about spontaneously channeling cures. That's probably a pretty minor thing to nitpick, though.
The only things I worry about balance wise (without having examined the book too carefully and without having playtested, and so on) would be:
(1) The non-good necromancer class which automatically reincarnates whenever killed into an animal with a really powerful template with the ability to turn human again whenever needed. This seems like it could be quite powerful.
(2) The lack of Armor Class enhancing spells (giving them costly material components means Shield is a lot less likely to be used, for example) or much heavy armor at all seems to make everyone's Armor Class significantly worse. Everybody does gain a feat that could possibly add a couple of points to AC, but I don't think it makes up the difference. The only problem with this, is that I don't think the chance to hit people is decreased at all, meaning that a certain balance of power has been dramatically altered, possibly meaning that every fighter-type character will want to use Power Attack all the time. But maybe that's a false impression; I'd have to playtest the game to know for sure.