Hi lord_hydrax,
I am currently experiencing the same issues within my SCCM 2012 SP1 environment. Were you able to resolve your issues at all?
I have a support case open with Microsoft regarding this who have remoted in and collected a bunch of logs and double checked on my PKI set-up and SCCM config.
Same set-up as you, Offiline root CA with Enterprise issuing CA. All windows clients are happily using PKI.
All appears to be text book. I believe they are setting up a LAB to try and re-create and have escalated it to the product team for resolution.
I will keep you posted when i receive an answer from them.
Regards
Matthew