OK I think my USB drive theory was wrong, however I just watched the duplicates appear.
Here's the sequence of events that happened.
1. Yesterday cleared out library again, no duplicates.
2. Today Went into Audio. According to the status bar there was 11.9 days worth
of Music which is about correct.
3. Placed CD in drive, and ripped CD (one cd only mind).
4. Went back to Audio, status bar jumped up to 13.4 days worth of music,
went to a snow patrol album, and sure enough Duplicates had arrived.
During this time the USB drive was never unplugged, the machine not restarted,
MC not exited etc. Whole thing was seen in less than 10 minutes.