pfSense

I have noticed this before when upgrading a slow system (like Alix 2D13). After getting the upgrade it tells you the firewall is upgrading. You click the pfSense logo every now and then, getting the same message - as it is still writing the image to the slice and doing its thing with it... good.
Then it sets the package reinstall flag, as it wants the system to do a package (re)install when it boots.
At this time, clicking the pfSense logo brings up the Package Installer dialog, asking to confirm the reinstall of all packages.
Obviously this is not a thing that we want a user to click at this point - the firewall is actually about to reboot and do the package reinstall itself.
One solution might be to have a different flag-file to indicate a package reinstall after reboot - then the ordinary GUI package reinstall dialog would not be triggered by that.