Without logs or the ability to reproduce it, there's not much we can do. I ran the install and it put the variables in the right place, so it's not happening all the time.

The install logs are usually detailed enough to see why decisions like this are made, but it'll almost certainly be because of something specific to your machine. If running the install again produces the same result, those logs will be helpful as well. I don't see us being able to make any product changes for this though.