Keep up the good common sense! And don't become discouraged, much less anxious, if your daughter has a setback now and then. There will be, as you've already discovered, some bumps in the road. In that regard, the fact that she's waiting until naptime or nighttime to poop is no cause whatsoever for concern. It may take a while — several months, perhaps — but this will eventually resolve itself. In the meantime, celebrate her success and pay little to no attention to her reticence to use the potty for pooping.
Having said that, there are some strategies that might move this process along. One especially creative parent folded a diaper in the bowl of the potty and told her child that the doctor had said he should poop in his diaper that way. The child promptly pooped in the diaper-lined potty and continued to do so from that point forward. That's a testament to thinking outside the box if there ever was one!
It's also interesting to note that before the 1960s, when everything parenting in America began to go to Hades in a hand-basket, parents generally poop-trained before they pee-trained. Also, potty seats attached to the seat on the big toilet, so when a child was on the potty, he couldn't get off very easily if at all.
When a child was on schedule to poop, his parents would put him on the potty and walk off. When the child pooped, he called his parents. They'd come in, help him down and clean him off. In other words, on-the-floor potties are part of the problem because children can get off them at will (but the advantage, of course, is they can also get on them without parent help). The sorta-kinda good news is that newer (but in my estimation, somewhat less effective) versions of the “old” potties can still be had. I found some on www.diapers.com, for example. You might want to consider that option.
In any case, stay the course. In the final analysis, patience will be the cure!