It’s my feeling that changing the properties to something other than their original media settings are why you’re running into problems.
Since you’re starting with DV-AVI, I’d leave the project settings at NTSC DV (720×480, 29.970 fps).
It’s when you go to render that you choose the various options such as 320×240, etc.
I just tried what you want to do with an HDV file (project properties set to HDV 1080-60i – 1440×1080, 29.970 fps) and had no problems customizing any of the WMV templates to the settings you described.