I’m a Softimage user too, but not a guru. First, in what format are you rendering out the movie file? I have found that Softimage prefers image sequences or AVIs but not Quicktime movies. Try rendering out a PNG sequence with a straight alpha from AE. You can extract the alpha with a channel picker node in Softimage.
The radio waves effect generates the waves on a transparent background, much like a particle effect. You just need to either add another white solid under the layer that has the radio waves effect – OR – add the Solid Composite effect to the radio waves layer AFTER the radio waves effect in the stack.
It’s because you are using “full-screen” when you RAM preview. Not that you’re doing anything wrong, but I confirmed on my machine that it does the same thing if I preview full-screen. I’ve never used full-screen mode for previews so I never noticed it before but this appears to be a bug. What version of AE are you using? I would suggest reporting it as a bug at the link below so they will hopefully get it fixed if it isn’t already.
Also, if you have Mocha for AE, it does a great job of tracking masks, although it does take a while to learn how to use it. There are plenty of tutorials on their website, the cow, and elsewhere.