Potential issue: Apparently /etc/profile is not replaced if modified. Can someone verify if this is fixed or not? I will investigate further as I fear it may be a pacman bug - if so, I'm guessing keeping etc/profile in BOTH backup arrays for the time being may fix this.
I can verify that this wasn't fixed on my update. My /etc/profile was still my original one and I ended up extracting the etc/profile from the filesystem package by hand.