Flats intonate a little bit sharp compared to rounds on the same bass, so it can take a little playing time to get used to it. It doesn't take long, but some can be put off by this thinking that suddenly something's wrong with the bass or strings or something like that. That, and the new backwoods-of-Appalachia-washtub-bass tone of flats can help prematurely get the flats off it and the rounds back on.
As far as playing them, flats don't respond as well to plucking near the bridge for the Jaco-esque tone, as a set of dead rounds. So you lose that when you go to flats.
But you gain so much thumpy, papery, cardboardy goodness with the neck PU going to flats, as well as getting rid of most if not all of the muaah too. So there's a lot to be gained as well.
L