When comparing databases on a Windows MySQL system, the table create script seems to include the AUTO_INCREMENT value.
The table comparison then picks this up as a difference between tables.
Looking in the comparison window shows that the AUTO_INCREMENT is included when there is data in the table.
This does not occur when comparing on a Linux system, even though the result of 'copy CREATE to clipboard' includes the AUTO_INCREMENT on both systems.
When comparing a db on a Linux system to one on a Windows system, the AUTO_INCREMENT is included only on table create on the Windows db.
It would make sense that the AUTO_INCREMENT=xx part of the creation script should be removed before comparison.
(I can provide a backup that demonstrates this behaviour if needed)