Well it dosn't sound like a problem estimating yardage but definately a form issue. From reading your post it sounds like you know hat's happening. IMO the best way to correct it is to practice, practice, practice and when you've got that shot in front of you actually think about it.

If you practice the shot enough it should become second nature but you might just have to remind yourself as you anchor to keep your bow arm up until the arrow hits the target. It's not a quick fix but you should be able to overcome it.