Edit: Ok, here's what's going on;
Genshiken Second Season (both volumes from what I see) is bugged on Amazon Kindle Bookstore so it is not in the Comic Book format that amazon uses, causing it to bug out on Kindle clients (and probably on Kindle Fire Devices)
Other Kodansha items (Or at least Genshiken Omnibus #2) are not affected, you can tell if a volume is affected if it can be downloaded with the Kindle Client for Windows 7 or Mac (as comic books are not supported using that client as of current)
So, for just now, if you plan on buying Kodansha manga on the Kindle Store, check to say if it says "Available for these clients", that's your hint that it's not a bugged book. If it says "Optimised for larger screens" then it's bugged and should be avoided until sorted by Kodansha.