I had a similar issue with a character prop.

Character was holding a bread bun parented to one of the finger joints, I then had a sausage parented to the bread bun and finally after this I had duplicated the bread to use elsewhere. The sausage was also a duplicate of a few sausages.

Any way, no idea where amongst the layers of grouping/duplicating it went wrong but my bread bun was showing a non existent duplicate in my batch renders, seemingly only after the frame at which I had duplicated it onwards...

So, if it's any help my solution was to remove the object (being duplicated in batch) from any grouping then used a parent constraint instead.

Hopefully someone has a better answer than this, Id like to know exactly what to avoid next time. I'm on Maya 2011 btw.