Swen told us in some interview, that this is suppose to feel like you enter the area, and sudently GM asks you to roll perception.
You dont know why ... its just a hint that there might be something there.
It seem to me like its working perfectly that way.
If that's the case, then you should be rolling when you enter the room, not just when you get right up on the thing you might be able to find. I would be totally fine if it rolled perception for every room/area, the first time each character entered the room/area, whether or not there was something to find. That way, it's not tipping you off that you're missing something.