When you set/create a prototype for a Page Layout, the  items in the "New Content" area (when browsing the site with admin on) don't preserve the prototype settings, however, when you go into the admin panel and browse the asset tree, and select the prototype from the New Content menu they do work and show the correct.

This is only on Page Layouts and not any of the other Asset Types that are prototypes.

I replicated this in this demo site:  http://demo.plainblack.com/demo1180538157_815/home

Basically, the prototypes exhibit different behaviour inside and outside of the Asset Panel browse mode.

Here's what I did: 

I created an article prototype.  Clicked a few settings, committed and saved.  I went and used the prototype to create a new article from Browse Mode.  Look at the setting for the Article being created with the prototype.  Now go into the Asset Panel, and create a new article using the prototype you created, and look at the settings. 

Why do they keep the same settings in one place, but don't work in another?

We have tried this for a couple of different Wobject types and still see similar beahviour- I think page layout are the only ones that work both places.  Most of the other wobject type prototypes don't work (behave different in browse and asset panel mode).  We have used the folder, collaboration, and article prototypes.