puppies are now 6 weeks old; they have their open whelping box and a large run in the house and more outside and are frequently out of the box.  There are newspapers and vet bed in the box. i had been putting puppy pads down to absorb some of the urine and to be honest some of them were using it.  i appreciate these pads are for a single puppy once home and so they quickly became a toy and were pulled around.  Their run is on a tiled floor and in the mornings their bowel movements were along the perimeter (ie far away from their sleep area). HOWEVER this week it has all changed and they are defecating in the box and sleeping outside in the run.  My assumptions are either the tiled floor is nice and cool OR the bed smells despite frequent changes. 

I am open to any suggestions - as still maintaining as normal a family life as possible.  ideally i want them to poo outside the box!

According to my dogs breeder, all the litter did the same as yours, the first litter that had done this.

Having heard about yours doing the same,I've come to the conclusion that it could be something todo with the hot sunny weather.
It was the same steamy hot summer when Isla and her siblings were about the same age as yours, so there could be a connection. Drove the breeder up the wall scrambling into the covered area to clean up.

For sure, all dogs will prefer to lie on a cool floor when the weather goes stupid hot.  With our litters, we had two 4 X 4 sections, the one with pig rails round three sides and the other not.   Puppies were in the pig-railed section, in a completely other part of the house and the floor (which was off the ground - and the sides were roughly 2.5 high) was covered with newspaper and with vet bedding over the top.   Obviously outflow was minimal and dealt with by mum.

Once the litter was up and around and certainly by week 3, the original section was moved into the kitchen and the second 4 X 4 section added.   That one had a hinged door.   The whole floor was covered with layers of newspaper which was regularly changed, and anything that arrived when I was right there, picked up.   As most of our litters were born into the better weather, we had an outside pen and they'd spend part of the waking day out there at which point I did a complete clean out of the whole box.   It still got rather rank towards the time they went home!   I couldn't have them running around out of the box (adults) however.   So the box wasn't open, other than to let mum come and go.  

I'm afraid it's just fact - having a litter of puppies means mess, and loads of WORK.   Not for the faint-hearted which is why we only did litters when we needed the next generation.   And why once they were all old enough to go to their new homes, those we weren't keeping, I was more than ready to see the little dears go! 

ps   Those we kept (usually 2, but once 3) went into a smaller area with a raised bed and tile floor - covered still, with newspaper.   We have never used pee pads.

I have found it much less smelly and easier to keep pups themselves clean by using shredded paper.  I actually shred junk mail and anything else needing shredding and store it.

yes it travels around a bit, but it is so much easier than sheets of paper.

As someone else said mine start of in a den like puppy/whelping pen, then on tiled kitchen floor have a pen double that size and from 4 weeks go outdoors to play where I have a covered 10 x 6 pen with a little upv doghouse. 

By 6 weeks the door is left open for them to have free run of the dog area, at which point the adult dogs take shelter where they can out of reach.

Once going outdoors they very quickly learn to be clean and at night choose one are of their pen as a toilet often not the are I prefer.

My friend had a litter a week older and they also chose to toilet ion the bed and sleep in the pen.

I removed the bedding out of the puppy pen and put a plastic plank separating off 1ft x 4ft out of an 8ft x 4ft pen. I put the newspaper in the fenced off area and caught one of them pacing around to go and popped them in the newspaper area. Left it there enough to smell and the other puppies followed suit. It worked pretty well and it stopped them a) charging through the poo during night time play and b) made it easier to get them going in the place I wanted to outside.