Joel,
Not sure yet
If you download the Twixtor 4.5 sample projects tutorial file in:
http://revisionfx.com/products/twixtor/help/#ae_compatible
I don't see any black at layer edges
Hard to say what is going on? Anyway you can send to techsupport at revisionfx dot com a comp with a few successive frames (not the rendered frames, the source and the comp with the mattes) to see what is happening?
Pierre