The Flash Player Plugin for Firefox needs to have the browser closed, where the one for IE no longer does.
If you open the Flash Player Plugin patch, say "FLASHPLAYERPLUGINv13.0.0.214", you will see a tab called "Custom Variables", if you go into that, you can choose to use Force Mode, Force Mode will force kill the open browser.
The patch will not warn users, but you could add a generic warning in your scan and repair behavior that can include something along the lines of "Please close all open applications, especially Web Browsers"
What we do is this, we (right click and) clone the patch, created a second one, with "Force Mode" added to the name. We set the "normal" one to Autofix and let it do its thing. For the cloned one, we push that out as a scheduled task at night as to not interrupt the user is they are using the browser.
As for the reboots, there is a "pending file rename" key that gets set when any patch or application is installed that the creator of wants to call for a reboot at the end. LANDesk looks to see if this flag is set, if so, AND if your scan and repair settings is set to reboot if needed / always, it will call for the reboot. It does not matter if the patch just failed or not, if that flag was already present, or, if the patch you ran created that flag, you will get the prompt.