In case anyone has encountered such an issue, which looks like can appear also on HTC Desire HD and possibly on other devices, here is how I managed to solve it.
I have moved background-position by 1px up and lowered shadow position by 1px down (from bottom 100% to top:-19px). With those settings, background image is being cut 1px from top, and there is no "auto" border additionaly rendered.
footer:after {
background: url("../img/shadowup.png") repeat-x scroll 0 -1px rgba(0, 0, 0, 0);
top:-19px;
content: "";
height:20px;
width:100%;
left: 0;
position: absolute;
}