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Make sure your Macaroon buttons are all macro buttons, and not action ID buttons. Action ID buttons use the Blizzard action slots, so if you have two buttons assigned to the same action ID, changing the spell/ability on one of them will affect the other one.
Are you using the "Dual Spec" checkbox in the bar config window, or the dual spec switching feature of Macaroon Profiles?
With a dual spec bar, you should not see any buttons moving when you switch specs, only the contents of buttons.
With dual spec profiles, make sure you are saving your profiles after you make any changes. Unlike most addons, Macaroon does not treat profiles as "what you are currently using". When you load a profile, it simply copies the profile's settings to your "current settings", and then anything you change is applied only to your current settings, but not to the profile, unless you manually go in and save your current settings to the profile.
Also make sure you don't have both features enabled, as that will probably cause issues.
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