I would suggest that you write a quick little OpenGL/Direct3D viewer to pump out the triangle data so you can visualize it. It wouldn't really be too hard to throw together, and it would let you move around to the problem areas and see if there are any loose triangles in the way that shouldn't be there. This would pretty much tell you if 1) you're reading the map data correctly and 2) if your quadtree is okay.
If those were both okay, then you could try and put your LOS code into the viewer. You could have it set up so you input two points for your line, and have it draw the line in red if there's a blocker or green if it's okay.
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