I read both the tutorials in the Wiki, but still can't diagnose this. The bunkers have fire and I can't click on them, but they're not invisible! Can someone open my map and look for it? The bunker triggers are the only triggers there? Thanks. I'm still not sure what the problem is!

BTW I also have a small Halo wav in there I made myself

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you have to detect them as cloaked before you can see them as cloaked (without a detector nearby). Buildings don't normally cloak, so you have to make sure the player you want to have (not) see the cloaked bunker sees the cloaked bunker, then remove the detector somehow. A detector can be a regular detector (turret, obs, cerebrate) or by sharing vision. Here's some examples:
http://www.staredit.net/files/573/
http://www.staredit.net/files/609/
http://www.staredit.net/files/106/

What rockz said.
The simplest way to do that is to disable them at map start and have a scanner sweep (not comsat station!) preplaced for the players.
The detection will wear off after a few seconds and after that the bunkers are fully invisible (except shadow).