First, lets clarify some fundamentals...
Does your bike have a one-piece seat? Or is it in two pieces? If it is in two pieces (rider and passenger separate) then you may actually have a Low seat. If you have a one-piece seat you may have bought a Low- BMW which is a different animal altogether.
If you have a Low seat on a standard bike., which is what I think you have, then the "fix" depends on some other things. If the Low seat allows you to have a comfortable reach to the ground when riding/stopping then the pain in the knees is not a factor of the seat but of the foot peg position. (Well- of course it is but lets not digress yet)
To solve this situation get a Peg Lowering Kit.
If you can comfortably and easily reach the ground and have the knee problems, then a regular seat may help. It will be thicker by some degree, likely about an inch. There are more guys trying to compensate from a too "thick" seat in order to get lower, so a seat swap ought to be easy to arrange, or look on eBay for a standard seat. Or even go to your dealer and see if they will arrange a swap, perhaps for a reasonable fee.