I am having the same issue with a an CRM installation file of 260 MB.
Problem:
The evolution skin extract feature does not see all the folders included in the zip
The extraction fails
Workaround:
Extract the zip on my local machine. Then archive it again as zip, now then re-upload it. After that the extract feature sees all the folders and extracts just fine.
There must be something wrong with the zip support because the archives are not damaged.