Batch render problems. Different results when rendering multiple frames...

[jasperh.92]

I have a simple scene with a 2d looking shape extruding back and revealing a set of rooms. The back walls then fly in and fill in the holes. When I render a single frame, the render comes out fine. 

BUT when I try batch render the whole scene I end up with the frames looking like this:

I animated the room extrusion with a blend shape, could this be a problem? Any help would be greatly appreciated. 

Thanks Guys.

[n8skow]

Are you using render layers or passes?

Are you able to upload your scene file?