Hi Brandon,We have been unable to reproduce the issue you describe. If Export Visible Layers Only is checked, the DWG file that is created contains only the visible layers. Feel free zip up your drawing and post it to this forum - we can check it out.
However, I'm just trying to understand what you're trying to do. It doesn't sound like you actually want to work with the file in AutoCAD, so what is the problem you're trying to solve by going through DWG?
e.g. Do you want someone that does not have Stardraw to print the file? If so, they could use the free viewer available at http://www.stardraw.com/products/OrderViewer.asp
If you can explain the problem you're trying to solve, rather than what you're trying to do, we should be able to suggest the best solution.