I don't think I would use floor leveling compound on top of the cement board. If it is just one seam, why don't you try and grind that piece where it is sticking up. If it's less than 1/8" it shouldn't take much. If you don't have any ridges sticking up, you should be able to get the tiles to lay flat. Use a 1/4" notched trowel and watch how you set them. That should provide you with enough adjustment.
The other thing Ben, how big an area are you tiling? Is the rest of the floor flat or do you have a number of dips? If the area isn't that large, you could take a 4' straight edge (level works) and find your high spots. You could mix up some thinsets and use it to fill in the low areas, checking with the straight edge as you go. If it's an old level, use it like a screed and pretend you are doing concrete. Let it dry overnight, scrape of any ridges sticking up and start your tile.