After updating, Windows permission settings are all messed up

I’m on Vista Home Basic 32-bit, and after returning home from a vacation, I was prompted to update Comodo. I did so, updating to 4.0, and now, the folder permission settings for my C:\Program Files and C:\Windows folders are messed up and I can’t change them at all. I’ve tried disabling components from Comodo and exiting it altogether, but I still can’t make these changes.

Please help! Quite a few of my programs are unable to properly run now that I’ve updated Comodo, and it’s really annoying!

After investigating my running processes, I forcefully ended a cmdagent.exe (or something to that extent) and it suddenly ended a lot of my running programs. Does this mean that all of them were running in a sandbox or something? I’m completely new to 4.0 so I still have no idea what’s going on.