Whenever I enter a building or such that requires a true transition, he disappears. When I go back out, he's gone. I can find him at 101 or if I fast travel, he comes back, but he doesn't follow me into building or other zone transitions.

I have Anchorge, Brotherhood, Zeta and Pitt installed. No mods whatsoever. I've tried exiting and reloading, but that doesn't help.

Is this a known bug and does it have a fix?

Wait an hour.

if your going into a DLC he wont follow you but if you aren't going into a DLC and just a regular building in the wasteland do what pistolero said and just wait an hour