So, playing around in DoomBuilder yesterday, I made a hidden teleporter that opens when some condition is met in the map. The front line of the teleporter (and thus the one with the Teleport special attached to it) is therefore a secret line that appears as just any other part of the wall it's on. (In other words, there's no separate door sector or hallway leading up to the teleporter -- a 64x64 unit sector just opens up; this is important to grasp.

)
So, long story short, marking the line with the Secret flag didn't work, because it still showed up as a teleport-colored line on the automap. Shouldn't the Secret flag override all other color changes?
I'm assuming there are other line colors that might also override the Secret flag (locked doors, etc), but I'm at work right now so I can't test.