@ThereRLG2006 I'm working on a Mac which unfortunately Stereo Movie Maker doesn't support, so I'm not that familiar with how best to work with W1 footage in it. I use Final Cut and After Effects for my 3D stuff.
If you google "fuji3D : fuji3D" the Yahoo! Fuji W1 group should be the first result... it's a discussion group for W1 users. Very knowledgeable people on there, they could tell you why you're having trouble.