Title says it all. It seems to be random and is really annoying.
3 Answers
Pokemon will be sent to the last active box (i.e. the last box that you looked at). If this box is full, Pokemon will be deposited in the next box up (e.g. if your last active box was Box 23 and it is full, Pokemon will be sent to Box 24).
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You had the most words in your answer (1 more than Ben's). Plus Ben has too much rep already :P Thanks!– KecoeyCommented Nov 5, 2013 at 23:05
It's the last box you left the Organize Boxes/etc menu on or, if that box is full, the next box with available space.
To avoid them being dumped in the wrong boxes, move your PC back to the "dump" box (which I usually put at the front of the boxes)
It sends to the last box you had open at the PC. If it is full, it moves to the next box until it finds an open slot.