Movie Capture Animation flickering

Okay heres my problems So I have this animation and it works grate if I use the Sequencer todo my animation but if I use Blender3D to do my animation it never comes in good its something with the baking of the animation has a bug in the FBX export. so I used Maya todo the animation and i got it to work grate :). Now if I use the Sequencer to play the animation it works too but now on movie capture animation is flickering and the objects are invisible this is a big problem because I can’t use FBX animations