I've just been looking back at my pups weights around 5 weeks. Both my girls had 11 pups in their litters and they wasn't the biggest pups and I did loose some, but Phoebes litter was a nightmare like yours, I was too and fro to the vets and they were on antibiotics and the works.
From the first litter I had a tiny tot who only just over 1kg at 5 weeks whilst the others were well infront of him, but he was as active as the rest. Then in Phoebes litter by 5 weeks all of them were only just over 1kg but again by 5 weeks they were all as active as each other. I do know you need to trust your gut instinct if you think something is wrong, may need to go back again and see a different vet for reassurance.