How about (just a guess), it's got something to do with the new über-whites with their IS Mode 3, that keeps the IS off until the shutter button is pressed, then turns it on just for the photo?
It makes framing (apparently) easier when panning for wildlife and runners etc, but there's got to be some sort of time needed between pressing the shutter button and the shutter operating, in which the IS elements start to work to stabilise the shot.
Maybe with the shorter time lag the IS might not function properly?
In which case, either the camera takes a blurry-ish shot, or maybe it waits until the IS is stable before firing the shutter, resulting in that 'variable shutter lag'?
edit, or yes, it could be the aperture stopping down, didn't think of that...