James, check this option, it may be the files are being replaced but the feature tree is showing old data. Open the part from within the Assy and see if it actually opens the newly saved item.
Other place to look is dismissed messages, as i know there is a pop up message when Save As with references is invoked, perhaps this has been dismissed and it is using a previously selected default.
I do have the Update component names checked:
I also had the message center cleared:
I have been replacing the saved as component after I create the new one. Even then the tree won't necessarily update (it is spotty). After closing and opening the assembly, the part is updated (but I have to do the replacement).
An added update, when I perform a save a copy and open, the copy doesn't open. It is created on the network and opens with the proper geometry.
Instead of "Save As" try "Make Independent" -> save with a new name..
The same idea as Save As but may work better.