[Doctor Death]

I went back and looked and I think the line that can fix this is

document.write('<div id="slashpage" style="position: absolute; z-index: 100; bottom:90px; left:275px; color: white; background-color:$vboptions[splashbgcolor]; border: solid 1px black;">') //Main splashpage container

The "Z-index" is apparently the order of the "stack" of windows...

Usually HTML pages can be considered two-dimensional, because text, images and other elements are arranged on the page without overlapping. There is a single rendering flow, and all elements are aware of the space taken by others.

In CSS 2.1, each box has a position in three dimensions. In addition to their horizontal and vertical positions, boxes lie along a "z-axis" and are formatted one on top of the other. Z-axis positions are particularly relevant when boxes overlap visually. (from CSS 2.1 Section 9.9.1 - Layered presentation)
It means that CSS style rules allow you to position boxes on layers in addition to the normal rendering layer (layer 0). The Z position of each layer is expressed as an integer representing the stacking order for rendering. Greater numbers mean closer to the observer. Z position can be controlled with the CSS z-index property.

So, you either edit the number by hand or you change it to a configuration option. Will try to edit it right now.
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Update: Tried changing Z-index to 1000 and didnt work, still was embedded behind the Flash header.