I've found out why the 3 hookpoints aren't working, or weren't working last night.
The must have all the same ID's in the database. After logging in today, and visiting my house, I found an Albion Teleporter at all 3 hookpoints I was having a problem with (minus the craft hookpoint). Quite annoying to have 3 NPC's that won't work, and having no ability to pick them up. Lol.
Paying rent seems to work, so do the notices. (Got a notice on one of my non-house-owner characters, as well as the house owner.
House vault also seems to hold items through restarts.
Will bring guild into the Guild House later, and try to break it for you guys.
