Take a look at the image below:
[Blocked Image: http://img.photobucket.com/albums/v221/deathcrush/crate_colourloss.jpg]
On the left side is a simple single brush crate with textures applied, no problems there. However, I wanted to add a bit of detail to the usual square crate so on the right I made the cover and rope attatchments as a masked texture and applied it over the original crate (with modified texture to suit) and extended the side so it looks more three-dimensional. Unfortunately as you can see, despite the fact that the textures are pretty much the same, the masked one has a lot of colour loss (which is strange because they both look the same in Hammer).
Anyone know why this is? 
The lighting in that shot is fullbright but the same problem occurs when there is light applied too, most irritating.
Also it occurs with masked models too, look at the green plant in this shot:
[Blocked Image: http://img.photobucket.com/albums/v221/deathcrush/jungle_test3.jpg]
It's missing colours, this is the model in HLMV with the skin texture on the right:
[Blocked Image: http://img.photobucket.com/albums/v221/deathcrush/j_plant.jpg]
What am I doing wrong 