For those of you who can't see beyond the Stone Age, your stones will need to be lapped. Lapped when you buy them. Lapped after using them a time or two or few. If you are rubbing your razors on rocks that aren't flat, your bevel won't be flat, either. When you are honing a razor, correctly, you are actually doing some fairly precise machining. If your tools are out of calibration then of course your results will be sucky.
You might look at your rocks and think they are flat. Or flat enough. No, eyeball flat won't cut it. Some guys will lay a straightedge on a rock and look for daylight underneath it. Meh. Better than nothing. Or you can lay your straightedge on the stone with two pieces of paper under it, on either end of the stone, and try to slide a third piece under the straightedge at various points between the other two pieces of paper. Or you can just go ahead and lap the rocks. The lapping itself proves that the stone is flat.
Here is a stone that is obviously dished. You should never let it go this far! Well, I did, but this stone is only used for very rough work.
The best way to lap a stone is to lightly glue a sheet of good sandpaper to a very flat surface, and work the stone on the sandpaper. Often a grid of pencil lines is drawn on the face of the stone, and when the grid is completely gone, the stone is presumed to be flat. For better results, this is repeated with a new grid drawn, because the slurry that develops as the stone is ground flat will pool under the stone and "erase" the grid before the stone is fully flat. The second iteration should only require a dozen or two laps. I use a 12x12 plate of 3/4" cast acrylic, or else a polished marble or granite tile. Ceramic is NEVER flat enough. I usually do not bother with the grid. I just watch the new surface develop on the high spots and spread across the stone as the high areas get knocked down. You can do this dry, or wet. Dry is more precise. Wet is a lot faster. You will want a bronze bristle gun cleaning brush to "card" the sandpaper when it loads up with slurry. A toothbrush can sort of work if you hit it every 5 or 10 laps. For glue, I recommend a spray adhesive, LIGHTLY applied to the back of the sandpaper. 3M or LocTite brand, either one, works great.
For best results, do not overrun the edges of the sandpaper. Overrunning can contribute to dishing in the final surface. This is why I recommend against the use of "flattening stones" for lapping. They are usually no bigger than the stone being lapped, and so there will of course be considerable overrun. A skilled practitioner might not have a major problem with this. A beginner definitely needs to stick to the sandpaper method.
So there you have it. Remember, when you first get it, a stone (except for a diamond plate of course!) needs lapping. After you use it a bit, it needs lapping again. Some guys lap automatically after every razor. Some wait until the unfortunate condition of the stone in the first pic on this page. I generally start with 120 grit sandpaper unless it is just a quick refresh, then go 320 if the stone is rated at 600 or above, and then 600 grit for stones over 8k grit. For just a touchup to make sure it is still flat, you can start on 320 or 400 grit paper. I like the red resin type wet/dry paper. It lasts a long time and rinses easily if you use a water drip.