Can you tell if the document made it into the repository at all? After running the process, you could try running a search for any new documents created in the last few minutes. If it's there, see if you can tell which folder it got saved to and if that matches what's configured. Also check the variable values for form name and case name for that instance. Based on those, what SHOULD the document be named? Is it what you expected. 

My guess is the document got saved to the repository, just with a different name or in a different place than expected.