Hi Chye. Yes I agree, it does seem that the auto_increment_increment is the one causing this.
If you are using master-master database, the two settings we are discussing cannot probably be changed.
It has been a while since I've looked closely at this, but I do not think Moodle supports Master-Master database setup. In fact it broke Moodle on older versions a few years ago when master-master db is used, and more than one front-end web application servers are accessing two different databases. If you are using Moodle with master-master databases in this way, you probably cannot safely change the increment settings. To this point, it is also highly dependent on what type of replication is being used between the two databases.
At this point I would recommend some caution. Find out if you are using a master-master db setup, where both master databases are being used simultaneously. I think it is important to understand this before making any changes. Also a database backup will be very important to have before making changes. The reason I am advising so much caution is because the id numbers are so critical to Moodle.
If you are not using multiple databases with master-master, and it is currently working fine, perhaps no change is needed. Though based on my experiences from a few years ago, I don't recommend using auto_increment_increment.
If you have a "young" site that is not in production, or just in "testing/evaluation" phase, then perhaps starting with a clean slate, a fresh install, is in order. My worry is that continuing as-is may end up with irreversible and unrecoverable damage to the db. Again this all depends on: if you are actually using a master-master setup, if both masters are being used simultaneously, what replication engine is being used, Moodle version, plugins that may behave differently, and probably more considerations.
I would like to find more recent information on Moodle and auto_increment_increment. I did a quick search and didn't find what I was looking for, something more from a very technical developer perspective.