Try reattaching the overlays to the brush face; sometimes I've had that mess up for no reason I could tell.
To do that, select the overlay (the little blue box shown in the middle of it), and press Alt+Enter. Choose "Brush faces", click the "Pick" button and click on the brush face it should be attached to. If the overlay overlaps several faces, you can Ctrl+click to select them all.
Anyone else using the 3d view in hammer with shaded texture get those annoying scale/rotate issues with translucent textures/decals/overlays etc. Like you can move around a trigger box and it'll be normal looking sometimes and then sometimes it'll be weirdly displayed (texture-wise). Also ever since that january SDK update, closing hammer lags my entire comp. I don't know why everything is just slow after I close hammer, or even when hammer is running and I'm going through C drive etc. I'm on a quad core cpu, but I'm using vista, so that might be the cause.