How funky...

At first reading you post I was wondering if you went through all the history one at a time after applying an Action that went bad - you'll see when it goes bad, and be able to figure out what it was that made it go sideways.

I'm wondering what would only work on jpegs (and I imagine bmp and tif) but not on png...

What if you were to save your images as tifs with an Alpha - would that do the job of cutting out your rendered objects instead of rendering with a transparent BG?

I'm interested in hearing your results - sorry I couldn't be more helpful.

-Lew