I wonder if the intended meaning was: "Not all ceilings are white"? In English, we can say, "Ceilings are not always white" to mean that, but in Esperanto, "Plafonoj ne ĉiam estas blanka" would give the idea, as you've suggested, that ceilings don't remain white. The meaning, "Not all ceilings are white" would (I think) be "Ne ĉiuj plafonoj estas blankaj" in Esperanto.
The given order, "Ceilings are not always white", would be the most usual in English. "Not always are ceilings white" might be possible, but "Not always ceilings are white" sounds very strange. My problem with the Esperanto sentence, "Plafonoj ne ĉiam estas blankaj. " is that it seems to be saying that ceilings change colour, and sometimes they are white, and at other times they might turn red, or green, or sky-blue pink with red spots and green stripes!