@homeoftheben – I had the same problem with the PDF Embed stack for a moment. The stacks were visible in the ‘Edit’ mode, but not in ‘Preview’. What’s more, when I clicked on the stack, the Inspector was showing the name “Template” instead of “PDF Embed”.
I think this was something to do with the fact, that I was using the copy-and-paste method of placing these stacks on different pages (before I upgraded Stacks to v.3). Anyway, I just replaced them with fresh copies and they work fine now (unfortunately, I see no way to customize this stack into a Partial).