This problem is so complex, I'll just stick to the basic...
I manage a child domain, in which it's divided in 4 sites in AD. Each site has 2 DCs under this child domain. I noticed when applying a change in GP, not all the sites were being affected by the change. I found out that the actual GPO folder in SYSVOL wasn't being updated in the problematic sites. I forced replications (via Sites and Services) to no avail. I manually copied the updated GPO folders in each Sysvol folders in each DC. (which "fixed" that particular GP issue)
I then tested Netlogon. In each site, i created a text file in one DC in each site naming it "a_[site_name].txt" (i therefore created 4 different text files in the Netlogon folder) I found that the text files weren't all replicated everywhere (with the exception of one site, which had all 4 text files).
What I found to be interesting is that the Global Catalog DC did not contain any of the 4 text files (in the site where the GC is at, I created the text file in a 'secondary' DC).
I did dabble a bit in creating manual connections in Sites and Services, but didn't want to go to far. I'd hate to have that 'resolve' this since I'm sure there's a more underlying problem than "site A doesn't replicate to site B".
Environment: Windows Server 2008 R2
I know I'm missing something but this is a start. So, help is appreciated, as always.