2 things immediately come to mind...

1) - Temps? 2 months ago it was the middle of winter. were they too cold?

2) - Age? You did not mention the age of the rats. Have you allowed your breeders to go too long without replacing them?

Since you have a few "clutches" growing up now, I'd hold back all of those babies (unless there are more males than you need) and switch out some of your older breeders and see if the young ones do better.

I love how you referred to the litters as clutches. Gave me a good chuckle!