What's the trigger you use to make your bunkers and beacons invisible like you can only see the glow thingy (on beacons) and just a dimmed out bunker.
Set doodad state.
I think you want to disable the doodad state for the bunker/beacon but theres more you have to do and I forget most of it. I dont do invisible

There are lots of tutorials around the site, go look in one of those.
(My copy paste isn't working... I dont know how...)
Go to 'Tutorials Database', 'Triggers', and go to 'Invisible Bunkers'.
Well, if you're too lazy to look there, I'll tell you. First, put a location on where your beacon/bunker is, and then make this trigger.
Conditions:
Whatever you want.
Actions:
Set Doodad State: Disable 'unit' for 'player' at 'location'
That's it. But, if YOU are the player that owns the bunker, you'll see a cloaked bunker. If you want the beacon to have ONLY the 'shiny' part, you'll have to make the beacon for another player that doesn't have shared vision with you. Then, create a detector, wait for about 200 milliseconds, and remove it. voila! You should see a cloaked beacon with only the glow part. NOte: If you just 'disable doodad state' on some units (example: command center) StarCraft will crash.
So what your saying is that I should make the beacon and the bunker for like player 1?
And if you have a gunch close together, and some dont cloak, it is because SC disables the first unit it finds of the type you said at the location you said. So a unit could touch the edge of location, and it will get disabled instead of one in middle of location.
you mean the farthest left, then the most bottom

like so
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it will hit that . unit because it is the farthest left, then most bottom
more ex.
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[.][ ][ ]
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__ is a blank spot

Yeah, you will get unit detection if you look at the grid tutorial map.