A few hours after the last session I played I started up the program and ran auto import - it appeared to work, a number of hands were imported unfortunately I don't remember exactly how many - but it seemed like fewer than I had actually played. I then went to the sessions tab and organized it by time and found no record of the session at all (after clicking the refresh button). I restarted and still no sign of those hands, so I went to the manual import tab and manually imported from the processed directory. 1,600 odd hands were imported which was the correct number, and then they showed up in the hold'em section as you'd expect.
To summarize the auto import seems to have imported and processed hands without properly doing so and I had to manually import to get the hands in even though they were in the "processed" directory.