For items using Variants/Variations, the Add to Cart button code is an HTML form with menus/fields, so the cart button itself is actually an <input type="image" ...> which submits that form, rather than a regular linked image (<a href=...><img ...></a>) like regular Add to Cart and View Cart buttons.
Thus, you'd need to look for CSS rules applying to INPUT elements, and/or add a CSS rule overriding those for cart button INPUTs, like so:
input.ec_ejc_thkbx {border:0,padding:0;}
...OR just add a style attribute to each affected Add to Cart button, like so:
<input type="image" border="0" onclick="javascript:return EJEJC_lc(this.parentNode);" class="ec_ejc_thkbx" alt="Add to Cart" src="http://www.e-junkie.com/ej/ejadd_to_cart.gif" style="border:0;padding:0;">
