I'm not familiar with emicsoft converter, but don't see why he's going to mpeg streamclip as an intermediate step. I've googled emicsoft converter and wonder if it's as good as flip4mac. Sometimes you do get what you pay form.
in FCP, use file: export: quicktime movie (not quicktime conversion) with current settings. That will produce a quicktime identical to what you're working with in fcp.
Then use compressor to convert to a wmv. Flip4mac offers a variety of options which as I said cost according to the quality they'll output. go to finder: system preferences, other: flip4mac to see which you have.
http://www.telestream.net/flip4mac/overview.htm
will tell you what your options are.
figuring out the best compression options can be complicated but it's a big part of our world.