Ah… I’ll explain what ydnar said more generally. But first, check the ‘sticky’ topic at the very top of this board for the newest version of q3map2, NOT shaderlab.com, hon. Specifically, get 2.5.15 as of the writing of this post.
When ydnar said you don’t need func_groups to make the AlphaMod brushes work, he meant that AlphaMod brushes that aren’t part of a func_group will affect ALL vertexes they surround, no matter what entity (or worldspawn) they belong to. I.E. If you’re just doing a single alpha-blend effect somewhere using AlphaMod brushes, you don’t need to seperate out all those brushes into a func_group to make it work. You still can, but it’s not needed in that case.
However, if you want to have two or more brushes touching, and assign them seperate AlphaMod brushes, THEN you need to use func_groups to ‘group’ the AlphaMod brushes with the appropriate brushwork, otherwise AlphaMod brushes that cover one or more vertices where they overlap will apply cummulatively. I.E. AlphaMod 25 overlapping AlphaMod 50 will result in (0.25*0.50)=0.125 for the surrounded vertices. Sometimes, this might be what you want. Others, it definately isn’t what you want.
Basically, think of AlphaMod brushes as multiplication. That’s all they do. All vertices, everywhere, start with an ‘Alpha’ value of 1. AlphaMod brushes multiple the current value for all the vertices they are ‘touching’ by their value. 25 = 0.25, 50=0.50, 75=0.75, 00=0.00, check the AlphaMod line in the shader to get the exact number if you’re unsure.
Now… what vertices are they considered to be touching?
If the AlphaMod brush is part of worldspawn, and not part of a func_group, then ALL vertices they surround are considered to be touched.
If the AlphaMod brush is part of a func_group, they ONLY vertices they surround [u]in that func_group[/i] are considered to be touched.
That make more sense? 
