Did anybody find a way to make this work, I have a theme with exactly the same issue and cannot seem to find the correct page template to hook into. Is there another way to solve this? The forum main index and subsequent bbpress pages all display correct just minus the search box and login links etc. If I use the short code they do display correctly.
Did you ever get anywhere with this issue mate, as I have the very same problem it seems my search box vanished after installing buddypress and the un-installing buddy press. Now i have no search box and I am stumped!