As mentioned, if you are using a *Nix based Deployment Server and pulling from Windows Machines, the permissions will not get copied over.
Your best bet here is to set execution rights on the $splunk_home/etc/apps folder, and enable "Inherit Permissions" with execute bit set. This should set the execution bit on all folders above $splunk_home/etc/apps. One side note to this, it does set execute on all files. If you are running a secured windows box, this might not be ideal.
In that case, you best bet would be to write a powershell script that will set execute on $splunk_home/etc/apps/*/bin/, and cron that to run frequently, or manually run this everytime you push an updated app..
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