I also found that it helps to give each worker it's own upload folder. Before I did this different workers would sometimes try to create folders with the same name. Obviously one of them would fail (write error).
Okay, slight correction to this. There are two separate sporadic issues I'm dealing with.
Problem creating directory <path>. It already exists as a file
Problem creating directory <path>. Do not have write access
Creating separate upload folders for each worker was an attempt to deal with the first error. Unfortunately it's still occurring for individual workers within their own folders. For now I have stopped using dedicated folders just to see if that increases the folder conflicts.
The second error has to do with the Windchill method server service account and folder permissions on the worker. I do not understand why most of the time it could access the files just fine and then other times it would choke, but the solution is to run Windchill's services under a domain account with permissions on the CAD worker machine. Here are two relevant articles from PTC's tech support site:
https://support.ptc.com/appserver/cs/view/solution.jsp?n=CS33760
https://support.ptc.com/appserver/cs/view/solution.jsp?n=CS60687