I did some digging, and apparently this is a bug that occurs if you try to change more than 27 options. I don't know why that's the magic number, but it is. If you change 27 and save them, any future changes that go over the 27 limit will be lost, all other changes before the 27 limit will be retained. You may be able to rearrange your bindings by hitting the "Reset Game Preferences" option from the launcher, logging in, then logging out again. When you log back in, all your options will be back to defaults, but you can set them back up. As a work-around, try not to make more than 27 changes so all of them will save the way you want. Our QA team is aware of the issue and they are working dilligently to get it resolved as soon as possible.
We've uncovered an issue that hard caps the number of settings that can be modified in Diablo III. As far as I can tell, we should have it resolved fairly soon. :)
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