In the PhpBB 3 admin panel under the General Tab, under the Server Configuration section on the Cookies Settings page is the domain name you have listed there the same one that the chatroom is being accessed on? Also, what is the cookie path that is set there?
If X7 Chat isn't automatically logging the user in when they have a valid PhpBB session its usually because the chatroom can't read the PhpBB cookies for some reason.
I had the x7chat installed on phpbb 2.0.21 before. Because the forum also had the account switch mod installed, if a user switched accounts, their logged in account to the chat would change while they were in the chat room and viewing the forum. The community that I maintain actually uses this feature often and people switch accounts often. I'm thinking, though, that if the autologin isn't picking up the user account data from the correct table, this issue may be resolved by correcting that.
That's very interesting, I'm not sure how exactly this worked with the old system but I suspect this doesn't work with the new system because the new system caches the user's data in its own database tables and uses that rather than going back to the PhpBB database every time. Its somewhat pointless since I don't believe the version 2 port of this integration system allows you to use different databases, but in X7 Chat 3 caching the data gives a significant advantage (and that's where this integration system is from).
This is probably why you are seeing queries against the X7 Chat user table, after the user's account is synchronized upon login X7 Chat should rely only on its own database for the remainder of the user's session. As I mentioned earlier, not a huge advantage in X7 Chat 2 but in X7 Chat 3 this feature drastically reduces the number of queries that are run.