Texture Atlas issues Okay, so I started a manual unwrap on a model, did a lot of work marking seams, placing UV islands, scaling them, etc, etc. Blender crashed and I lost the work. I took a break, went  back to it, got up to the same point and instantly saved curse you blender and your naff session recovery.

Now that I've got my UV all set up and where I want it, I ended my manual unwrap, and it moved all the UV's as if they were fresh Unwraps, taking up the entire UV space for each object. Am I missing something?

For me it's: Select all the objects to unwrap, start manual unwrap, do the business and all that with UV space, come out of edit mode, end manual unwrap. Is that right? If so, what's going on with this unwrapping? Pictures to follow.
Check if you have more than one UV Map on the object
If your object already had a UV Map for some reason, TextureAtlas will simply create another UV map. In Blender, per mesh object, at the moment up to 8 different UV maps per mesh are supported. You can see a list of your UV maps in the mesh data tab of your object:

As you can see, by simply clicking at the names, you can switch from one map to the other. The render icon at the right determines which UV map gets passed on to the Texture Coordinates node in the Node Editor:

If the TextureAtlas UV map is all you need, just remove all other maps using the - Button.