Are you choosing New Game from the title screen, or loading a save file that might have been from an earlier version of your game where you had different equipment set up by default?
Are you using the Initialize option when you add them to the party?
What plugins are you using? I do seem to recall someone having a similar issue quite a while ago and it may have been a plugin that wasn't set up properly.
Finally, do you have any events that you've set up to change characters/equipment, as a way to speed up play testing? Could be that you've done it yourself, and just forgot the event was there.