I have experienced several issues in regards to meta-progression. The very first blob-monster, the one that splits into two upon death, is not registered in my monster archive. Again, with regards to archives i have an issue ala-this: 

I think it is worth mentioning that despite the individual archive stories being completed, seen as 4/4, the overall collection is seen as 0/8. I think there is some issue with registering and tracking this, since; like you said, i didn't have any unique epilogue either after beating the game again.