The only time I'll reorder my deck is if I'm reading in public. It's so I can make sure that no cards dropped out and are under the table. At home, I just leave it as is--but the cards for the last reading are usually at the top of the deck. It's just how I put them back in the box.
If I've reordered a deck and I'm going to use it for readings, then I always make sure to shuffle it thoroughly before I give it to the sitter or shuffle it for the sitter if I'm doing a remote reading. This helps make sure the cards are well mixed and randomized. That way, if a run shows up, I know it's real and not just a bad shuffling job.