Problems with copying applications to Applications folder

Hi all,
I'm facing serious issue's with Mavericks.
I'm a in-house developer, and I made a few apps that are bing used in process.
A few weeks ago I made an 'autoUpdater'. This checks a windows fileshare for any updates. If there are updates, it will copy this file to the /Applications folder.
Now the thing is, the current logged in user, which runs the autoUpdater, is able to run all applications which has been installed/copied.
When they log out, and another user logs in, all those applications show up as Zero Bytes, And seems damaged or incomplete.
However, when I copy the 'damaged' app to the users desktop, its working again.
Back to the 'original' user, the app is fine in /Applications.
Even after running Disk Utility from boot usb, to repair permissions, problem is not solved.
chmod 0775 on the application, does not work
chown root:staff on the application does not work
touch application, does not work
all these things combined, still not working for the newer users that login.
I've also done all this manually, and it does not solve the issue.
Anyone have any idea's ?

Hi LexSchellings,
installing applications I do for all users.
The problem goes when I'm copying .app files to /Applications.
If I do it from my 'autoUpdater' application, or manually, it does not work.
There is an little application called 'Permissions Reset', which actually fixed the problem, but I have to do that manually, I need to do this by terminal commands, because I'm talking about updating a small application for 1500+ desktop / laptops and they never are all on ;-)
My application checks for new updates when they boot up.

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