You have to drag the files in when the archive screen is up. Switch over to Explorer, find the files, drag them onto the CK's taskbar icon, then from there to the archive box. Don't let go of the mouse while doing this.
This is the process I use when updating my stuff and it works fine.
It won't automatically pick up meshes and textures that don't have referenced data in the CK. You will have to do that manually each time.
That was pretty cool Artmoor.
I got an error that it failed but when I used BSA Browser all the files were, in fact, there.
Actually I just split the screen with the CK on the right and Explorer on the left and just dragged what files I wanted to include

It's a lot easier than using the archive utility.
Thanks!