Are you using a mod that depends on ACE Timex? I never did sort out exactly what caused it, and many never had the problem, but I found that Timex overrode my character settings every time I logged on with Timex enabled. It wasn't that settings were lost, it just didn't use them, and defaulted instead of going to the character specific settings. I disabled Timex and all was well. It's just something to look into - may have nothing to do with your problem, but it sounds pretty similar to me.
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