Fixed is the way to go but I am not sure what other things are impacting try the below styles.
#header
{
position: fixed;
top: 0;
left: 0;
z-index: 1000;
background: rgba(255,255,255,0.95);
width: 100%;
height: 3.5em;
line-height: 3.5em;
text-align: center;
font-family: 'Open Sans Condensed', sans-serif;
font-weight: 700;
text-transform: uppercase;
}
#footer span
{
position:fixed;
bottom:0;
width:98%;
float: left;
height:14px;
background:#0c609b;
text-align: center;
font-size: small;
color: white;
clear: both;
}