It was my understanding that doing a guild run in a dungeon would give everyone guild rep and give guild xp, but shortly after the last patch 4 guildies and I ran blackrock caverns and got zero rep and zero guild xp (and the drops were the same agility item but that's a separate issue). 4 of us were level 85 and we had one at level 82. He got regular xp but like us received no guild xp or rep.

We also did not get a guild achievement for running it together -- We only got the personal achievement for it.

Is this still not fully implemented? or did I not understand the explanation of guild rep and xp right?

This data did not make the last patch. This functionality should be live in the next build.