Good Question! The reason you're uncomfortable has to do with "balance". Most drummers just wonder what's wrong but never think that the culprit could be the throne height and many times it probably is.
Well, there is no set height in inches, but there is a "correct" height. It all starts with balance and weight distribution. If the throne is too low, you'll have the tendency to lean backwards. If it's too high, you'll start to lean in on the kit. Both of these senerios are undesirable for many reasons. For one, it makes your legs and feet work much harder than they need to. It will also cause you to rush fills and have other time and "pocket" problems.
The trick is to think of your buttbone as your center point. That's where you want the fulcrum for your weight. Now you have to experiment to find that height that allows you to lift one or (preferably) both legs off the ground without feeling like you have to lean forward or backwards to compensate. This gives you that ever allusive "independence" between all of your limbs. It is virtually impossible to keep good time or play fluidly if you're off balance.
One other variable in this is your front-to back position on the seat. Again, experiment until it feels right to you.
That magic height may feel strange for a while, but pay attention to how your leaning through variuos parts of a song and use that feedback to adjust. Hope that helps.
Mark