I've looked at this. So far no real clue. The maddening thing is that the code that triggers single suffix in the non directory case is the same in freebsd's bmake and ours, so obviously it doesn't trigger when there's an extra directory, as the paths don't match.
I'll have to check if there's some sanitization of prefix that I haven't found yet. Still the most convoluted part of that program... :(
