Greetings:
Sorry for the delay in response. I have been out of town since last Thursday.
I have to admit that I have not put any effort into exploring the cookie issue or timeout settings. However, after reading your post, I went to the PHPBB website and read a little on it. All of the settings for the RF Cafe forums regarding cookies, timeouts, etc., were left at the default settings. The help recommends leaving them at default unless multiple forums are being hosted on the same domain.
One thing I did just do is change the cookie name from "phpbbsql" to "phpbb_rfcafe" so that maybe it has a more positive identification. When I look at the cookie that gets set on my own computer, it is listed as "rfcafe[n].txt", and has this opening text when viewing the cookie contents, "phpbb_rfcafe_data".
The timeout is at the default setting of 3600 seconds (1 hour). I do not know if that is what causes your unread post list to clear after a certain amount of time, but it does not seem like that should be the mechanism.
I'm open to suggestions if you know of a better way to configure the settings.
One thing that I should do is update the bulletin board to the latest configuration (from 2.0.5 to 2.0.8a), since that might help clear up some of the inconsistencies (like sign-in not always working the first time). I've been a little hesitant because things have been running fairly smoothly so far and I hate to give it an opportunity to screw up. The other thing is that applying the patch to permit voting in the polls without registration was a painful process, and will probably have to be re-lived after upgrading to the newer version. Maybe I'll try it out tonight.

Thanks for writing.
- Kirt B.