I think your github repository is missing files.
Please could you specify what exactly is missing ?
I downloaded a copy from github for a fresh install to test. On permission page it was showing few files were missing..mostly flash.
With same setting 7.2 official works fine but not the github version.
Nathan Paton
Looks to be:

The following files and directories have inappropriate permissions
Elements Current level Desired level
media/images/classifieds Not Exists Writable
media/moxie/files Not Exists Writable
media/moxie/storage Not Exists Writable
flash/modules/board/files Not Exists Writable
flash/modules/chat/files Not Exists Writable
flash/modules/photo/files Not Exists Writable
flash/modules/im/files Not Exists Writable
Nathan Paton
Made an issue on GitHub:
It should be fixed now:
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