Some filesystems lose the executable bit when a file that is marked as executable is checked out, or checks out an non-executable file with executable bit on. git-clone[1] or git-init[1] probe the filesystem to see if it handles the executable bit correctly and this variable is automatically set as necessary.
A repository, however, may be on a filesystem that handles the filemode correctly, and this variable is set to true when created, but later may be made accessible from another environment that loses the filemode (e.g. exporting ext4 via CIFS mount, visiting a Cygwin created repository with Git for Windows or Eclipse). In such a case it may be necessary to set this variable to false. See git-update-index[1].
The default is true (when core.filemode is not specified in the config file).
git update-index --chmod=+x
This might solve your problem. This Modifies the index or directory cache and Set the execute permissions on the updated files.