Bump!
Since I have updated my hardware i got this problem. I got sierra 10.12.4 (had some problem on 12.3 as well) Its persistently asking me from time to time (every 2 days maybe) for transmission, xee, unarchiver and some other applications that "You are opening the application for the first time".
I have tried to solve it by running this command on the terminal:
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -r -all local,system,user
Which doesnt solve the issue. Im suspecting that something in the system is deleting related files from time to time and I have no clue whats causing this. I wonder if I should change anything in my clover settings or bios or anything else in the installation.
Any ideas?