could be lack of flow, could be low spots of co2 in the tank, or uneven lighting.
First the lighting, i would re position the two lights so they are on the sides pointing more or less straight down, this will be much more even spread and equal par, and thus rule this out/fix any lighting issues.
inadequate flow has a large impact on co2 distribution, as well as nutrients, so maybe the rocks are blocking flow and slowing it down in those areas, maybe flow is fine but co2 isnt reaching it very well. co2 isnt always equal throughout the tank, just cause the drop checker is green, doesnt mean there is 30ppm of co2 around the substrate, it could be much lower. my suggestion would be to ditch your current co2 injection method, and spend the $10 on a proper diffuser(your running pressurized co2 i think?) this will give a much better mist, and place it opposite your hob. every other week or how ever often you feel, you can swap which side your hob is on, this often helps kick up mulm that gets trapped as well, and can change co2 flow in case there are low areas.