So could you describe me exactly what happens please ? Wait... you are playing a shaman... I'll look to something this way.
1. I login with my shaman, both main and off-hand weapon buff set to "None".
2. I set a buff to each weapon, and mousewheel works fine.
3. Log out or exit game then check SimpleSelfRebuff.lua in the SavedVariable folder, both weapon buffs are saved.
4. Re-login and check the setting, they change back to "None", so I have to set again.
I dont know whether other classes have the same problem.