Wow, you have a better memory than I do! Yep, this is the same old automate problem I had before. I had set the project aside and now I have a deadline to meet.
I'm checking Override Action "Save As" Commands, and choosing File Naming as "Document Name"+"extension". I want to use the original document name, although I don't have to, if choosing something else makes it work.
What it's doing is, opening file_1.tif, saving into proper folder as file_1.jpg, opening file_2.tif, saving into proper folder as file_1.jpg, opening file_2.tif, saving into proper folder as file_1.jpg, and on and on. And the one photo that always appears in the folder is the very first one it opened.
And yes, I had a problem with the CF card door sensor; bought another used body, and I've been using it ever since. I really do need to get that broken one sent back to Canon...