We laid fiber-cement board on the floor (tore everything up, down to the subfloor) , it's in thinset, but the seams won't lay flat and we want to lay 18″ porcelain tile on that. How do we get rid of the bumps? Can we put leveling compound on top of the cement board or grind the seams down?
It sounds as though when you put the thinset down it was not applied evenly or some of it was to dry. When this happens the thinset will not allow the cement boards to lay flat and smoosh the adhesive flat when they were screwed down. The result is the uneven edge your now dealing with. Also poor mixing will result in clumps that will not allow the boards to lay flat.
If there are only a few joints, I would pull those boards up, scrape the old thinset off and reinstall new. My concern is that there are voids where the cement boards have been placed as some areas are suspended on the dry high spots while other areas there may not be any support. The result if you were to level with compound or even built up the thinset under the new tiles is that this will begin to move and cause cracks making the project even harder then now to fix.
If there are lots, then pull them as well. The seams of the cement boards should be even. When applying these boards, be sure that the thin set is loose enough to trowel evenly. If you find that the stuff is thick like peanut butter, throw it away. Thinset is cheap enough. Also do not mix more then you can use in about 15 min. Once you set the boards, Screw them down. Do not put a bunch down then go back to fasten. Be sure to use screws every six inches to assure a good bond.
Sorry there is no magic fix for this other then experience.