
We had a pup in a litter last year with the same problem, checked for CP etc. he was passed as ok. Always sounded rattly, took him in the bathroom and LOTS of snotty muck came out. It wasn't until he reached 6 weeks that WE found he had the tiniest of hole in his soft palate, something that couldn't be seen when he was tiny as it was quite far back and so small, but as he got older it got slightly bigger.
When he was on a milk diet, milk would come out of his nose and I was convinced (although I couldn't see it) that it was CP, once he went onto a dry diet everything seemed ok. He's now 17 months old and just had the hole repaired and is fighting fit.
Fingers crossed for your little pup, but do keep an eye on things, my pup had been checked by 3 different vets and they ALL missed it.
Good luck.