well, make your window brush/patch detail. Default is structural, which may cause unwanted portals. Not sure if portalling is the reason why everything behind the window vanishes... Could also be a texture problem, some textures require an underlaying, solid texture to show as intended.

You can also try adding a clip brush (brush with tool texture clip glass). Or redo the window brush, texture it completely with caulk or maybe nodraw, then assign the glass texture to the front and back. In BSP this can make a difference, 'cause the surface properties will be taken into account - in this case of caulk / nodraw.