As a workaround, can you avoid writing values to the database if the size/shape is impossible under normal conditions? That way at least the last valid position would be used.
I know it's hard to tell if the position is off-screen, but these windows are getting sized to an impossibly small value as well. When I do reveal them, they're only big enough to show just the upper-left corner of the Navigation pane. Drag the lower-right corner of an Explorer window up-left until you can make the window no smaller - that's what I see. I'm sure you're seeing the small size values in the database.
Oh, and for what it's worth, on TechNet I'm hearing people not using your tool reporting the occasional opening of Explorer windows off-screen. It may not be something your tool is doing at all, but rather a Windows bug that you are then propagating to subsequent window positioning. Food for thought.
-Noel