hijinksensue, I ran into this problem too.

What you need to do is go into your es_input.cfg and make sure that your buttons refer to page up and page down, similar to the following example:

<input name=”a” type=”button” id=”4″ value=”1″ />
<input name=”b” type=”button” id=”5″ value=”1″ />
<input name=”down” type=”button” id=”1″ value=”1″ />
<input name=”left” type=”button” id=”2″ value=”1″ />
<input name=”menu” type=”button” id=”13″ value=”1″ />
<input name=”pagedown” type=”button” id=”11″ value=”1″ />
<input name=”pageup” type=”button” id=”10″ value=”1″ />
<input name=”right” type=”button” id=”3″ value=”1″ />
<input name=”select” type=”button” id=”8″ value=”1″ />
<input name=”up” type=”button” id=”0″ value=”1″ />

After the auto configuration in Emulation Station, my buttons seemed to refer to top left and top right or bottom left and bottom right.

Hope this helps!