There was a discussion in a thread a while back about seat assignments duirng the auto-upgrade process. It appears the upgrade list is processed from the back to front, left to right. So if 4A is available, upgrade 1 gets that seat. If 4F is also available, upgrade 2 gets that one. Upgrade 3 would go to 3A, etc.

Your seat preferences are not taken into account whatsoever during this process.