Just to close off this thread - it was just me being stupid…
The fact that I posted this “It seems to try to search for the root directory e.g. “E:” rather than the actual file name…” should have given me a clue.
I normally have my files in a particular directory where I produce the cover sheets and then copy everything to the drive attached to the WDTV.
Because I had quite a few episodes to process, and still had a few to obtain, I copied the episodes into the root directory of another drive. By doing so, I mucked up the directory structure and ThumGen didn’t now where to look for the Series name etc.
Once I fixed up the directory structure everything works fine.
I think I should go to bed before I make any more stupid mistakes 
