Possibly same for Windows binaries.

Not windows binaries I confirmed that on Linux already. I'm having the same issue see http://feedback.arma3.com/view.php?id=16648 same issue with the files not sure on that command to fix it yet will test tomorrow morning or tonight seems to be the same issue.

Same issue on Linux files

Can you try renaming the 'keys' directory to 'Keys'?

I get ban now when it verifies key from my server and it's on verify = 2 weird I can play on other servers but not on my due to it will auto ban me now=.

verifySignatures = 2 - will result in a ban

verifySignatures = 1 - will result in a ban

verifySignatures = 0 - Playable

I can verify that partly.

If you got all files in the root where steamcmd.sh installed that, then it is working (I got the cfg files in a subfolder, that is ok).
If you do it like here: http://erictgrubaugh.com/play/games/arma/installation-and-configuration-of-an-arma-3-linux-dedicated-server/
It will not work, so I guess there is a problem with the links, so if you make a subfolder with links to the root folder/files, it is not working well.

@Nasdero Can't verify that, got a vanilla ds linux install with minimal config running and it still kicks clients off, even though addons match bit for bit, symlinks ain't the issue. My guess is the hash function for linux is broken.

Sry I have no more Linux installed right now.

After lowercasing all the signed keys in the keys folder, verifying and updating again, it seems fixed on linux DS after Apex, finally.