Kim I know this must be frustrating, but it does work, and that's been confirmed not only by myself but others in the other Logic forum who were asking why they couldn't hear the click in their bounce. They all chose "REALTIME BOUNCE" and it worked. So something is different in your setup, I'm not sure what it is. My main outs are 1-2, I bounce to WAV, 16 bit, other than that I can't think of anything odd that I do. I actually did it by soloing a track with nothing on it, turning on the click, and doing a realtime bounce. The resulting file was a click. I'm using the MPC click, for what it's worth. Logic 8.02, System 10.5.4 (but it's been working like this for several systems now). The click is assigned to 1-2. Make sure of course, that you have "Click while playing" chosen. If I think of anything else I'll chime back in....
Tom