I have this issue when I fly SYD-SFO-LAX return or similar. I always CALL IN to res and ask them to apply SWU only to INTL leg and then I wait. If the INTL leg clears, I ask them to apply to domestic leg. I would hate to waste a SWU on a domestic (unless, like last year, the darn things wouldnt clear, so I did throw them on mid cons and trans cons for friends and relatives) .