I don't believe this used to happen and it's driving me batty!! I save a working document in a job folder. Then when I go to collect the fonts and graphics by "packaging" it won't allow me to package in that first level it creates another folder inside the job folder with the same document, same name along with the fonts and graphics folders. Needless to say having mutiple files with the same name is REALLY DANGEROUS!! I am positive this is something new that is happening. Probably something easly to fix - I just can't find it!
It has always been this way. You can create the package folder anywhere you like, and there is no real danger in the duplication unless you lose track of wheter you are working onthe packaged copy or the original, but that's up to you.
That's exactly how it's supposed to work and how it has always worked.