System REBOOT - closing tables - repair

[oldengine]

Everything is functioning properly, but when my server goes through a REBOOT for maintenance updates automated or otherwise, I encounter the following situation:

After the REBOOT, running a MySQL check on the vBulletin database brings up several tables with the following error:

myuser_vbul.adv_gallery_categories
warning : 1 client is using or hasn't closed the table properly

myuser_vbul.adv_gallery_customfields_entries
warning : 1 client is using or hasn't closed the table properly

myuser_vbul.adv_gallery_images
warning : 2 clients are using or haven't closed the table properly

Is there a way to prevent this other than a ***MANUAL*** repair of the databases throughMySQL Account Maintenance?

Is there a proper way to gracefully shut down MySQL prior to a reboot?

A MySQL "repair" fixes everthing, but not until I manually intercept the situation.