In photoshop under layers, you have rgb layer and alpha layer (if you don't see an alpha layer, click the button top right of layers pane > create a new layer > alpha).
Anything in the rgb layer will not effect transparency weather it be chroma or alpha. Everything in the alpha layer will effect transparency.
In grey scale, black is transparent, white is opaque. grey (if used around the edges) will give you a soft edge on the transparency, but is only effective with alpha transparency in dxt3 and 5, preferably dxt5. dxt1 with 1 bit alpha will only give you 2 colours (shades) in the alpha layer, if its black and white, it will be full opaque or full transparent, if its grey it will be slightly transparent.
Chroma only accepts 2 colours in the alpha layer, anything not white will be transparent (I think) anything white will be opaque.
This probably what you are doing by the sounds of what your saying,,,
If you don't set an alpha layer but have transparent areas in your workspace, then save as dxt1,3 or 5 with alpha, the alpha layer will automatically be generated using the transparency in the workspace. But you should really set your alpha layer up manually.
One other thing I forgot to mention, edge blend was another tweak I used along with mip bias to tune in the chroma transp.
[ED] actually, now I think more abotu it, I think anything in the alpha layer not black will be opaque with chroma. I'd have to do some tests to make sure, I will double check this in a little while.