When starting Aegean in Flames on B1258.2, all Greek Naval forces around Cyprus, SSM installations on Cyprus, and several other subs and Greek naval units are Unarmed. I suspect an overzealous rebuild, unless I misremember the scenario.
Save game file attached.
I'll lay down a second install of the current production environment to compare against, because I'm a glutton for punishment
Cheers,
-J