I, too, have whelped my share of puppies but have never seen this. The closest I have seen has been a litter that was born five or six days prematurely whose feet looked bright red when they were born, but the color in their feet returned to normal after two or three days. We never did figure out what it was and everyone acted normally and nursed normally, and, as I said, by two or three days after whelping the puppies looked normal.
My best advice would be to get these babies to a vet to make sure their circulatory systems are OK and that everything else is OK with them. As with anything that can't be explained, acting quickly might prove to be what resolves the situation uneventfully, so I wouldn't wait to take them in for an examination. Please let us know what the vet says.
Ghilly
I've done my share of whelping puppies but have never seen this. I would think it could certainly be the way they were positioned in the uterus and that is a good size litter. Sounds like it *may* be a circulation issue. I would think if it were a heart issue of some sort, you would be seeing other symptoms. Are they still purple or are then getting back to a normal/pink color? I don't think the massaging would hurt.
How old are they now? Do they seem healthy otherwise? Nursing, defecating, etc?
If it were me, I would at least take those two pups over to the Vet for an examination.