The first thing I would do is to lift the flapper and feel the rim for any imperfections which would stop the flapper from sealing properly. The second plan of attack would be to inspect how you installed the flapper. Did you use the extended ears which are attached to the overflow tube? Does the back of the flapper seal correctly in the back, towards the tube? Lastly, is their enough slack in the chain to the flapper to allow a full seal or is it a little tight, not allowing the flapper to seat properly?
If all of the above is adjusted properly, the flapper should seal correctly. If not, you have two choices. You will need to either replace the entire overflow tube and flapper seat, or you just might need to look at other flappers other than Kohler brand to see if they seat better for you.