When I'd update settings for one of my roles and click store all the role settings would dissapear for that role. When I looked in the database the permissions were there, but duplicated several times. In the end I figured out that I could fix it by running the database clean script in update/common/scripts/. As usual I'd recommend you back up your database first though :) It seemed my problem was caused by a buggy database upgrade script, though I don't know which one as it'd been updated many times.
Hope this helps,
Regards,
~James~
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