CTF: The Duel for JK (and the MotS conversion is identical in this regard) has the Rail Detonator in a special place.
Notice the "top floor" corridors that are above the ground floor (containing the flags).
What you should do is get on the upper level and look for the cross bridge in the center of the level (the one where the Concussion Rifle spawns). Between it on either side are a spawn point for the power boost and the super shield on the opposite side. Go for the power boost side, and you should be able to jump THROUGH the wall (there's an invisible panel). Once you jump through there's a small elevator and switch, as well as a Super Shield, a Rail Detonator and two bacta tanks.
Normally such a powerful secret would probably unabalance the level, but this is CTF we're talking about, so while you're loading up somebody can snatch the flag. But you CAN snipe through a little window on the bottom level, and people can't see you on the other side.
Actually the way I found this was I was playing with a group and (I think it was Krayt Tion) got blasted by the splash from somebodies weapon and he went THROUGH the wall. I was shocked, and then I noticed rails flying through the wall at me. He then told us where he was and we figured it out.
Pretty sweet if you ask me, it changes the whole dynamic of the level knowing where that secret is.
In the MotS version it's a little easier since you can rely on Soldiers to bring Rail Detonator's to the level. ; )