That's normal. On my phpbb3/pp pro install, phpbb3 shows 406 members and pppro shows 411 members. The reason for that is phpBB3 only counts the number of active users. The old version just counted everyone. I didn't check the code but I assume PP Pro just does a count of the users with no check to see if they're active. Chuck will be able to verify that.
No action is necessary, there is no "synching" of the total number of members.