I spent some time earlier this week trying to debug a permissions problem in Drupal.
After a lot of head-scratching, it turned out that Drupal assumes that when you run INSERT queries sequentially on a table with an auto_increment integer column, the values that are assigned to this column will also be sequential, ie: 1, 2, 3, …
This might be a valid assumption when you are the only user doing inserts on a single MySQL server, but unfortunately that is not always the situation in which an application runs.
I run MySQL in a dual-master setup, which means that two sequential INSERT statements will never return sequential integers. The value will always be determined by the auto_increment_increment and auto_increment_offset settings in the configuration file.
In my case, one master will only assign even numbers, the other only uneven ones.
My patch was accepted, so this problem is now fixed in the Drupal 7 (and hopefully soon in 6 as well) codebase.
The moral of the story is that your application should never make such assumptions about auto_increment columns. A user may run the application on a completely different architecture, and it may break in interesting and subtle ways.
If you want to use defined integers like Drupal does, make sure you explicitly insert them. Otherwise, you can retrieve the assigned number via the mysql_insert_id() function in PHP or via SELECT LAST_INSERT_ID() in MySQL itself.
Have you checked your code today?