Nothing running (consuming CPU) in the Processes tab; this is what I meant when (along with the Applications tab) I checked Task Manager in step 3.
I have now sussed the cause though, thank you; my 1TB Seagate FreeAgent Pro eSATA drive. If it's powered up I need the aforementioned double turn off to get the PC to power down. If it isn't running*, then the PC powers down on the first turn off command.
*The eSATA drive doesn't display in the "Safely remove hardware" window (though the three internal SATA drives do!) so I tested my theory simply by pulling the eSATA cable out (eSATA is theoretically hot swappable anyway) to switch it off; the PC then shut down on the first "turn off" command. Pulling the power lead out of the eSATA drive had the same effect; one click PC shutdown.
Now I know the cause I will simply live with it as it's no great hardship.