Hi Dale,
When researching the book references for Dave Shepard earlier today I came across a photo of same in Fredie Charles's book -"Conservation of Timber Framed Buildings". These square holes are not just restricted to crucks and can also be found in other types of early building especially large aisled barns. The reasons for these holes cannot now be proved absolutely but some have taken a stab at their likely use with most postulating that this has something to do with raising but that might not be the case.
I am sure that Cecil Hewett showed us some examples of these in the Barley Barn at Cressing Temple during a Guild visit some years ago. He makes reference to these raising holes (now plugged) in "English Historic Carpentry" page 62 where he provides his own explanation about how these were likely used albeit a little difficult to understand without the aid of a drawing.
I have also found plugged holes in the centre of the sides of large tie beams in early medieval buildings suggesting that they were probably gripped with tongs when being raised using a single point lift.
Regards
Ken Hume