And while I'm on the topic of custom locations, I have the following scenario.
The app launcher "app.exe" in "app" folder for historical reasons launches "app\bin\mainApp.exe". I added AutomaticUpdate control to mainApp.exe and set wyUpdateLocation to "..\wyUpdate.exe" (placed it in root "app" folder according to the docs). If I launch "wyUpdate.exe" by hand, everything works fine.
Inside the app the update control spins, but gives the following error: "wyUpdate ended before the current update step could be completed." It does launch wyUpdate.exe in the root folder, but nothing good happens...