Re: AUTO_INCREMENT seeding not working intermittently

[Rick James]

InnoDB? MyISAM? (It may make a difference.)
Was the server restarted between the ALTER and the first INSERT? (It probably makes a difference.)
Did you DELETE or REPLACE any rows? (It may make a difference.)
Are you ROLLBACKing any transactions? (That 'burns' an id.)

I ask all those questions (and more?) because they have an impact on AI calculation, and in an ENGINE-dependent manner. For example:
After a restart, the next AI will be MAX(id)+1.

As a workaround:
Skip the ALTER. Instead, INSERT a row with an explicit id=499999 just before doing the real INSERTs. Optionally DELETE it, but not until after some INSERTs have been done.