As to your second question:
What might be the difference cause?
The simple answer is: time and sugar content.
Natural bee honey is an over saturated sugar solution with some additional ingredients the bees pick up from the blossoms. Over time, especially if some of the water content evaporates, the remaining liquid cannot dissolve the amount of sugar that's already in the solution any longer. The liquid sugar is forced into a solid state and forms small crystals. That is the “rough texture” you observed in the lighter colored honey.
The darker honey will start crystallizing as well, but when exactly that process starts depends on the sugar and water content and on the variety of honey. Wikipedia states:
Within a few weeks to a few months of extraction, many varieties of honey crystallize into a cream-colored solid. Some varieties of honey, including tupelo, acacia, and sage, crystallize less regularly.
In that respect, I see no difference in quality between the two samples of honey. This is simply how natural honey behaves.
It's possible to dissolve the crystals in the lighter honey by putting the whole glass (without a lid) into a water bath / bain marie and gently heating the honey until it's liquid again. The sugar will start crystalizing again after a few weeks. Adding a few drops of water (and I mean individual water drops, else you risk turning the honey into sugar water) can keep the consistency smooth for longer.