Submit a bug report from the affected character with the grimoire please, that'll let us pull a snapshot of the character so we can see what's going on there. Weird since I recall that coming in and us addressing it, so it'll help to see your particular case.
The Vault is completely separate from any of this, as that's mainly Rob and the UI team working on that. Other than my having a few meetings about it, the data file team hasn't spent any time on it. Once we get it fully set up though, it should save us a fair bit of time when entering content, which should free us up more for other tasks.
Okay, so you're seeing archetype skill feats appear in the free archetypes table, when they shouldn't. Probably a side effect of a fix I made a while back, but an easy fix.
What's the ancestry feat?
I get the frustration though, and wish I could instantly fix everything. There's a lot of tasks I have logged to make improvements and expand functionality, and have been trying to keep us reasonably on top of bugs, but it's all juggling time and tasks.