Yeah, I remember that. I suspect you misunderstood what func_areaportalwindow is for. It's not, as the name suggests, for putting in windows as opposed to doors. It's for when you want an opening to fade to a solid texture after you get a certain distance away to save even more on rendering — mainly used for (solid) windows because you don't have to worry about getting shot through them. A good example is that one window in Thunder Mountain's third stage. (If you've played enough Thunder Mountain, you know the one I mean.) So probably this is what happens when you don't set the fade distances or place an associated func_brush like it expects.
TL;DR just replace it with a regular func_areaportal and don't worry about it