Yeah I start all my wow's via their .exe. However when the patch hit I found that when I patched up my main as normal.. then copied the wow.exe and wowerror.exe as I normally do on patch day.. only 1 of my screens worked. the others errored out or would go to the download screen. Since this was a tools patch, the wow.exe didn't change.
So I looked at what did change and saw that the launcher, repair and I still can't remember what the third item is in the main folder, but those 3 things changed. so I then just copied and pasted those 3 items to my other folders and I was back in business. I relaunched my games and none of them tried to patch anymore or gave me errors.