I guess some example images would be useful as I am not sure what you are getting.
So, when you render a single frame, does Bloom and Glare show up in the VFB? Does it show up in the PV? For B&G to appear in PV for an animation sequence, it has to be set before you begin rendering (you can adjust B&G in the VFB and the current frame in the PV will update, but any previous frames in the PV will not, the B&G is baked in to those).
The batch script, I think you mean for processing the CXR in post. However, you can't save to CXR from the PV at the moment, so that wouldn't be an option when rendering an animation (as animation output can only be saved from the PV).
If you could show what you have in the VFB, what you have in the PV, and describe your workflow, that would help - unless the above already gives the answer!