by Ken Task.
Run servers with several moodle installs using the same DB server. Since I'm the only one via command line, I do sometimes use only ONE DB moodle user to access the various instances databases.
User: moodleuser
Has access rights to moodleADB, moodleBDB, and moodleCDB.
Each Moodle should have separate code, DB, and data directories.
Moodle A: code: /var/www/html/moodlea/ data: /var/www/moodleAdata DB: moodleA
Moodle B: code /var/www/html/moodleb/ data: /var/www/moodleBdata DB: moodleB
Changes in Moodle A are NOT reflected in Moodle B.
Now if I had mistakenly set the database for Moodle B to the database for Moodle A, then yes, there would be some behavoir such as you have described.
Check each sites config.php file for DB host, DB name.
'spirit of sharing', Ken