Afraid I can't be of much more help than that. Those are the only real circumstances I know of that determine whether or not the line is visible. The only other thought that I might have is that when I mentioned the TDC resetting on loading a saved game, it also resets the Distance marker to neutral, so if you're using one of the constant bearing attack techniques that don't use the stadimeter, make sure you're dragging that blasted little rangefinder triangle around before you send bearing and range to the TDC. That little quirk has caused me to miss a few crucial shots before.
If there are any other known bugs or glitches that can cause this, though, I'd have to defer to someone who's more intimately familiar with the engine, afraid I'm not all that much help there.