I was hoping to have an answer to that question before someone asked it :P
It's been puzzling me too, in my mind, the ideal thing to do and indeed the thing I actually do in play is to punch out another cp builder and get a "head start" on the next cycle. However, for reasons I'm still investigating, this sims out as a loss of around 1.5k dps. This could simply be an error in the simulation, but it feels odd that it was put there in the first place to compensate for it rather than fixing the bug as is. This leads me to believe that it is, in practise, the correct way of playing despite me, as of this moment, not understanding why.
Like I say, I'm still looking in to that one