I do 16:9 all the time. Not sure what's going wrong here, but it's not the aspect ratio.
As a rule of thumb, I make height and width both divisible by 16, although all WMV9 requires is divisible by 2. Maybe try something slightly different, like 352x192?
My Book:
http://www.benwaggoner.com/books.htm
Cleaner e-book:
http://www.cmpbooks.com/cleaner/
Compression Class at Stanford:
http://www.digitalmediaacademy.org/compression.html