What strain are you growing? Autos can be a little finicky and some of the new genetics off-kilter. What made you decide 12/12? How old are they? Any pics? Are they flowering right now? 16/8 should be fine for an auto at any stage, their lifespans are so short you really want to maximize light, most do 20/4 or 18/6, sometimes all the way through. At the same time, some find that their plants do require a change in light schedule and don't flower like expected, and that's typically when you'd switch to 12/12.
Buuuut, additionally, some people just go with 12/12 flowering and have success - and others go 24/0 the whole way. Haha, there are a bunch of ways to do it. Shouldn't affect them though, autos aren't all that responsive, if at all, to changes in photoperiod. At least they're not supposed to be, if the genetics are right, seems like they're still working out a few kinks with these autos.
16/8 should be fine, though.