Problem with table prefix?

I use different prefixes for my wordpress blogs and there seems to be a problem there. My users don't get Syncronised. I get no addition to the prefix_users table on my sub site. However, every time I press "Sync all sites now" on the main site I get two entries in the prefix_usermeta of the sub site. The entry is always meta_key = user_sync and meta_value=1

Any idea?