No, I've never added a download file and received the "empty" attribute. If the file name was typed incorrectly, there would be a red dot, which would turn green when corrected. Nor has anyone ever reported that while uploading one of their products.

I began Zen with 1.3.8a and have done every upgrade since, currently through 1.3.9e.

It's definitely a bizarro reason. LOL! One minute green dot, file names are there. The next, poof, they''re gone! Again, not all of them, only in seemingly random product categories, while random extras/empties appear elsewhere.