Boss man got on out GTM and explained the history of the issue. About a year ago they moved from FSR to DFSR for SYSVOL. Sometime after that, an admin who no longer works there, restored the main DC from a snapshot pre DFSR migration and pre adprep for 2008 R2. So you had the main DC now thought it was on schema 44 and the other thought it was on schema 47. One thought it was using DFSR and one thought it was using FRS. That admin attempted to trick the DCs thru a series or regedits and ADSIEdits. He then went and restored a copy of the SYSVOL tree to a file share and then copied and pasted that to both DCs.
They have been operating in this screwed up, unreliable, non-steady state for over a year now. Three months ago (I was originally told two) the new admin comes in to all this fiasco and also tries to reverse the travesty thru a bunch of regedits and adsiedits. Why no one thought or bothered to get Microsoft support involved over a year ago is beyond me. I talked the boss into us getting Microsoft support involved. My co-worker who got me involved in this call is now getting an AD backup and will open a call with MS. When he finishes up with MS support, I will let you know "the rest of the story". Thanks Webster