Nah, there aren't so many things that can go wrong
I'm pretty sure it's either a problem with kindletool, or a classical case of PEBKAC
... I'm also using OpenJDK, so this should not be an issue... and I've also compiled (and fixed) kindletool to work on my machines.
Kindletool is in a rather awkward state, so yes, it seems normal that it can't unpack the files it has itself generated. You may have realized that there is a previous commit saying "doing half of the KindleTool work myself" now. In fact, the tool is now creating the entire content itself (including all the signatures), kindletool is only used to "encrypt" the .tgz now.