Actually, I have been trying to find out a way too, and I figured out what to do!!! After reading your post, and how you mentioned moving table to users, I started to looked into our wordpress database. I looked for the name and id of the test account, tester, that I just created in any tables that have seems to be involved with either users, groups, or multinetwork. Turns out the problem table is the wp_bp_mnetwork_users. Here what I found:
1) There are the user_id for 2 admin, whom I think are the ones that login in during the last few days when I set up multinetwork.
2) There is a user_id belonging to my tester account. So, 3 users, nothing else. Hmmm…
3) The 2 admin have a network_id of 3 (our base site number, which is an overview site with no member listing), and the tester’s network_id have 2 (our latest site, which have both group and listing).
4) I changed the tester’s network_id to 3. It disappear from the member listing.
5) I added a new row, containing one of the admin’s user_id with a network_id of 2. The admin is now showing up in the member listing of the new site.
6) If I change or add a new row with network_id 1 (which belong to the old event site), the associated user would now appear in the old site’s member listing!

My solution was to do a MySQL insert:
INSERT INTO databasename.wp_bp_mnetwork_users (user_id, network_id, is_active) SELECT user_id, #, 0 FROM databasename.wp_#_bp_xprofile_data;
The # indicates the site_id, unless their site_id is 1. In that case, the first # is still replaced by 1, but the FROM table would be named “databasename.wp_bp_xprofile_data”;

I don’t know if that’s the best solution, since it does require user to have mysql knowledge, but it works!

We have 58 approved users in Site A. Site B has 9. There is some problem with registering users due to another plugin, but I will be trying to fix it tonight so I can test out what happens to the member list if a new user is register on Site B.

It was indeed a cookie mix up. Once I use 2 different browser, it works perfectly.
However, I encountered another problem. Once the groups were set up, the member listing says ‘Sorry no members were found’. Here is what I did so far:

1) My first thought was that maybe I was not in the user list of that site.
So, I went to Dashboard -> Users. My own user account is in both site’s Users page, so I guess I am in both user base.

2) Ok, maybe there is a problem with the user or group list separating the user base?
So I checked the number of users showed in the Dashboard->User page of both site. They seemed correct – my 2 sites have different number of users (Site A have 84, Site B have 9 since that the recent year with less registered users). My Dashboard->Group page shows the correct number of users in each group, too.

3) Well, may it is something in the front end?
I went to the group listing in the front end… and it shows that I have the correct number of user registered for each group! Yet when I go to the group’s member page, it shows ‘Sorry no members were found’.
What’s even more strange is that when I go the front end Members page to see all the members, it display the same error message!

However, once I disabled the BP Multi Network plugin, the list of member shows up again. But this plugin is what I used to set up different groups in different sites. Right now, the only thing I can think of is to disable the plugin and try to filter the display to show only certain group in certain site, but I am relatively new to BuddyPress, so I really hope to avoid doing so. Any suggestion is highly welcome. Thank you for your help.