"You are opening this application for the first time." Um, no.

[GanChan]

Over the past couple of days I've occasionally encountered an odd situation in which I'll open one of my usual everyday apps (such as Bean or VCL) and I'll get the "You are opening this application for the first time. Are you sure you want to proceed?" message. The apps themselves are behaving normally in every other respect. What could be causing this?

I'm running Maverick on a 2013 Mini.

 

[chscag]

I've had the same thing happen after installing a certain new app or updating an older one. The first time I opened or updated the app, I expected that warning (from GateKeeper) but with certain apps it persists. I found the only way to make GateKeeper stay quiet (other than shutting it off) was to do a reboot. After rebooting the message goes away. I don't know if that's what happening in your situation but try a reboot to make the message go away.

 

[AppleNewton]

Depends on where you may have gotten the update or possibly if the app is not stored in the applications folder. But yeah, updates may cause this if it thinks it's a different or new app or signed differently

 

[Samuelsan2001]

Over the past couple of days I've occasionally encountered an odd situation in which I'll open one of my usual everyday apps (such as Bean or VCL) and I'll get the "You are opening this application for the first time. Are you sure you want to proceed?" message. The apps themselves are behaving normally in every other respect. What could be causing this?

I'm running Maverick on a 2013 Mini.

A major updates or OS updates can cause this behaviour it is normal.

 

[colourfastt]

A major updates or OS updates can cause this behaviour it is normal.

This has become a problem only since the introduction of the "kindergarten OS's"; it certainly isn't "normal".