I've created a new hat (copy model update stats), so simple done it plenty of times in Fallout 3. Also ran autoarchiveinvalidated separately. Also ran Update Facegen model as well.
Nothing seems to get the hat to sit on the head properly. Could be something Steam overwrites when it runs or what?
Any tips or tricks would be appreciated.
Its not a steam issue, there is a bug with the Update Facegen function in the new GECK. Read this sticky from the Nexus and, it will explain how to fix your hat. You'll need FNVedit to fix the issue.
http://www.thenexusforums.com/index.php?/topic/250193-converting-fo3-hats-to-nv/
You'll still need to use this method even if your not trying to port a hat from FO3, It needs to be done for all new hats or, you'll never get them to sit on the top of your head.
hope this helps
cev