This is different from my previous bug which was fixed, and seems to have either been there but not noticed by me, or to have crept up later.
What happens: certain changes (but not all changes) to a proxy rig layer visibility are not preserved on file save / file load.

steps to reproduce:

1- download the file source.blend and save it on your disk.
2- start a new blend file and save it as 'scene.blend' in the same folder.
3- from the new blend file, link in the group 'Group' with relative paths + instance groups on from source.blend
4- press ctrl-alt-p and select 'Armature' from the list to make a proxy for the armature in the original blend.
5- note that layers 0,2,3,10,18,19 are visible in the armature; this corresponds to the state in source.blend.
6- save again
7- start a new file
8- load 'scene.blend'. Note the same layers are still visible.
9- turn on layers 1 and 17, and turn off layers 2 and 18. The new layers state is 0,1,3,10,17,19 are visible
10- save
11- start a new file
12- load scene.blend

If you have the same bug I'm seeing, you'll find:

13bug- layers 01,3,10 are visible only. layers 17 and 19 have been hidden.

What should happen:

13good- layers 0,1,3,10,17,19 should all be visible, as in step 9
I'm attaching a scene.blend file if you would want to skip steps 1 through 8, just save them into a the same folder to keep the links.

Operating system: Ubuntu GNU/linux 10.10, 64 bit version, running on a dual core and an 8 core Intel system, both with nVidia Graphics

revision 34288