Like I said, I can't duplicate the problem in my test project, so it's either a configuration issue on your end (action sequence, passive state granting extra attack times+, etc) or a plugin conflict with something.
From a test play if your project, outside of battle, open the console, and type in $gameParty.actors()[0].isCurrentlyDualWielding() . It should return a true or false (replace the 0 with the party position of the two handing actor, 0 being the first party slot, 1 the second, etc).
Then, go into battle and do the same thing again while in battle. Once again, the result should return a true or false.
In battle, there are many extra checks made, including if the actor has a two handed weapon, a shield, a barehand, etc, so it's normal for the function to return different things inside and outside of battle.