Yes, the .REG file should be in the FSX root folder. However, on Vista, if you installed FSX in the default folder, there might be some permission issues that might prevent that file to be automatically created.
However, the .REG file is not really needed. It's only use is save you from typing the serial number and perhaps typing it wrong. It's not read by the Addon Manager, and it's not needed for the activation, it's JUST an export of your Windows registry key that holds your serial, in the standard registry editor format. So, having it or not, it's not needed at all to reactivate a product.
So, if you don't have the .REG file, just select the "Register Serial" option, and type the Serial Number as shown on your email receipt. Serial Number, not Order Number...
Basically, the server-assisted Reinstall, the .REG file, and the "Register Serial" options do exactly the same thing: they insert your Serial Number in the Windows registry, and activate it online. How do you insert it: by asking it to the server (server-assisted Reinstall), by using the .REG file, by typing it with the "Register Serial" function, it doesn't matter, the goal is to just insert the Serial Number in the Windows registry so it can be activated. They are just 3 ways to do the same thing.