Today i had a very strange experience, i am sharing this with you to save you time.
I got a zip file, big one with many directories.
When i have tried to open it with windows default zip extractor i got 3 directories, although actual there were 10 directories.
When i have opened it using the free 7zip it worked, all the 10 directories extracted.
As far as i know this is Microsoft bug. Who know's, but actually 7zip solved me the problem.