Shaders : Only One Level Of Transparency?

I've been working on this map for awhile now, and it is getting done slowly but surely. I have, however, hit a bit of a snag while trying to get a shader working.

Basically, I need a shader to be slightly transparent, but after about an hour of messing with it I can't get it to change its opacity. Granted I haven't made a shader before, but shouldn't I be able to just change qer_trans to control it?

It does change in GTKRadiant itself, but once you are in the map it is either solid or at about 50% transparency, no matter what I do. :scratch:

Any insight would be most helpful, thanks in advance,

-Sonata