I have seen this issue before in the past, so I suspect the cause is the same.
You are using a weapon to enable dual wielding on the actor. Likely the mainhand weapon, based on what you've said so far.
During the attacks, each weapon is temporarily unequipped to remove all of the traits from it when it isn't being used. The offhand weapon is removed first, so the main hand swing will only use traits from the first weapon. Afterward, the offhand weapon is re-equipped, and the main hand weapon is removed so the same can happen with the offhand swing. When the main hand weapon is removed, your actor is updated to not be capable of dual wielding anymore, because the dual wield type trait is on that weapon. This removes his offhand weapon as well, causing him to continue the second strike, but with his main (bare) hand instead.
After this happens, checking in the menu will show the offhand weapon as unequipped, and likely gone from the inventory as well.
To fix this, add the dual wield type to the actor, or class directly, instead of to the equipment he/she is wearing.
