I made a little tutorial on making glass last night, but whilst I was doing it, I found that I could not replicate the effects in my main map, and just suffered the same problems as everyone else. I don't know why there it won't work in a simple map, but works in a much more complicated level. Oh well.
So I continued the tutorial using another method and wrote a little text file trying to explain it. Here:
http://than.leveldesign.org/files/glassTest.zip
There are two levels included and both are very similar. The second one uses a simple method for doing water and glass together that is practically fool proof, and the first one uses the original method but with the exception that I couldn't get the skip texture to work on the water brush so I left it as water. Here is another shot of my map to show how it should look (looks like all the other shots :)
http://than.leveldesign.org/files/basepack_s04.jpg
Anyway, I hope this helps someone, but I also hope we don't get tons of people using this effect in their basepack maps because I wanted mine to stand out as being a cool flooded level.
Biff: cheers for the textures, I will compare it to my wad tonight (that sounds deviant somehow) and replace textures in my map with any that are missing.
I think that when the pack is about done (mid-december) we should get all the idbase levels together and make any missing high res textures so that the pack is (partially, as it would only be idbase maps) compatible with Starbuck's textures... If you aren't already checking your map with his textures as you go, of course!