I'm no aegis expert but I think you can ignore those policy warnings, you'll get used to seeing them during a lot of package installations over time, you're only getting that during installs right?
If the package installs and runs as expected there's no need to worry,

That issue where the programs weren't showing I've never seen and I'm completely clueless about it, I probably wouldn't worry unless it shows it's ugly face again and starts to be a pain.
Good old reboot eh, that's one ridiculously common fix for all things electronic.