Some suggestions:
When setting up the hone with the guide rod, make absolutely sure everything is flat & straight. If you're not already doing it, lay the hone & rod flush to a dead-flat surface while tightening the rod in place, and make sure it all stays flat after tightening the set screw (sometimes it 'moves' when tightening down). Make sure the rod itself is also straight (not warped or bent); this can be checked in the same manner, by laying it flush to a flat surface.
Keep pressure as light as possible. Too-heavy pressure will bend/flex the guide rod, which obviously will alter the angle on each pass. Keep the pace slow and controlled, as going too fast will likely introduce some inconsistency as well.
Make absolutely sure the edge is fully apexed before progressing beyond the first hone. If it isn't, you might not notice it right away, during the coarser/medium grit stages. But, as the bevels begin to polish up during the Fine/UF stages, the polished bevels will really begin to stand out against the coarser scratches left on the untouched portions of the edge, near the apex. I think this is the most common problem encountered with anyone new to sharpening; very often, impatience will lead one to stop short of the apex. Use a good magnifier under very bright light, to make sure you're fully apexing the edge (form a burr) at the beginning stage, before moving on. Then keep re-checking it with each subsequent hone.
A possible, but less-common problem, might be that the ceramic hones (Fine or UF) aren't truly flat. Sometimes they can come from the factory with a little bit of warp/bend in them. Check them against a dead-flat surface (edge of a steel ruler, or against a good flat piece of glass).
David