Since you used my suggestion on the graphic file, I'd start there. Check the properties. You'll need to increase the color depth to at least RGB-8bits. Save it. Reopen. Then, take a background eraser, erase a small section of the file and then clear it out again. You will then have a totally transparent file. If it has any pixels at all and you didn't save it with the proper color depth, that could be your culprit.
You can check this by viewing it as a thumbnail in Windows Explorer. See if anything appears when you view it. (You still didn't tell me which graphics editor you are using, which hinders my advice a bit.)
IF you determine this is not a problem with the graphic itself: This code is located in the template.css and is most likely where you will find your solution:
/* Top */
#rt-top .search .inputbox {width: 236px;height: 20px;line-height: 16px;border: 0;padding: 3px 0 0 5px;}
#rt-top .search {text-align: right;}
/* Header */
#rt-header {position: relative;z-index: 2;}
#rt-header .rt-block {margin-bottom: 0;}
#rt-header4 {padding: 5px 0;}
#rt-logo {width: 236px;height: 49px;display: block;}
The display is showing only within the 960px portion of the template so I'm really leaning towards the graphics file itself, rather than the coding. If it is not the graphics file, it's got to be either a margin or a padding problem. Problem is, I can't tell if it's an overflow from the TOP or a glitch in the Header.
I'm thinking it's in the Header. The TOP doesn't show a margin or padding statement for the bottom of that section. Yet it "appears" to be coming from there.
I'm guessing it's in the Header statement.
I would try inserting "margin-top: 0;" at the end of the second line in the header section. If that doesn't work, take the padding down to "0" and see if that fixes it.
I hope that helps. Gotta' scoot.... a mountain of thunder and lightning here. Will check back later.
Carol