Thanks Henry! That's what it was. I don't ever remember it being an issue leaving it on when not shooting at long shutter speeds. I thought Canon said it didn't kick in until exposures over 1 min?!
There's two noise reduction systems. The first one is for long exposures. It can be off, auto or on. It performs NR for exposures longer or equal to 1 second (not 1 minute!).
The second NR system is for high ISO. It can be on or off. Canon warns about reduced maximum burst if this NR option is turned on.