Interesting!
The folder that Autocrat is placing these documents in, is this folder on your drive ( not a team or shared drive), is this folder already shared with others and/or is it nested in another folder?
Could you try a test with a new folder, placed on the top of your drive ( not inside any other folders) and make one or two docs with autocrat and see if doc appender can find it?
If you are still having an issue, could you copy and paste your user key form Doc Appender menu on this thread and we can check the backend for errors.
Thanks!!