I don't think that Spear Pillar, where Dialga and Palkia are captured, is technically considered a "cave" area, because once while resetting for a good nature, it became morning and my Dusk Balls repeatedly failed to work despite me False Swiping down to 1 HP.
That's odd, because I never got 'im down to 1 hp, just in the red as I can manage, and I average 5 dusk balls, in the morning, past 9am. Of course, I only did this about three or so times before I found a nice Palkia.