How do you edit within the zip?
I am running Kubuntu 12.04 and ARK will not let me edit anything in the zip, I have to extract to a folder first, make edits and re-zip, and then the installation aborts from cwm.
The stock archive manager within Ubuntu lets you do it. 7zip does as well, IIRC.
With those with that error, it looks more like to be an error with the source because it seems like a lot of stuff is missing. You could try the alternative method for Java, but I don't think that's a guaranteed slam dunk.
Did you folks sync with the branch or the master?