I don't think it's just a case of her _not_ wanting to use them(I don't believe, I could be wrong though, that they just can't pick and choose when they use the pads). It could be a retained shed on the pads or it could be that the gecko is going to shed soon. Spray it's feet directly with warm water and see if that helps.
Letting the gecko run around on a countertop is a BAD idea all around, between things the gecko could possibly be carrying and also the cleaners and chemicals on the countertop can possibly be harmful to the animal.
Also, you've only had the animal a month, it would probably be better if you didn't handle it for a little while, let it get used to its cage and new surroundings. I know some people like to handle their goldens, but they can tend to be a bit high-strung when it comes to holding them, and as you have already exprienced, they tend to jump out of your hands a lot and can get hurt from high falls. If you ARE determind to handle it, wait a few more weeks then SIT on the floor and go slowly. Sitting on the floor will reduce any damage that can be cause from falling from 4 feet onto a hard floor.
~Cro