After figuring out the problem, I wanted to share this to save some time for others who are having similar dilemma.
The following script will reset all containers for modules on all pages for a particular portal (in this case PortalID is 4) so the default container set in site settings would apply, show you the result, and roll it all back. This way you can verify that everything is the way you want, and then just run the UPDATE portion of the script to actually reset the containers. You can play with the SELECT statement if you want to check on other fields as well.
BEGIN TRANSACTION
UPDATE TabModules
SET TabModules.ContainerSrc = null
FROM (SELECT *
FROM Tabs
WHERE Tabs.PortalID = 4) T1, TabModules T2
WHERE T1.TabID = T2.TabID
SELECT T2.ContainerSrc, T1.PortalID, T1.TabID, T2.TabID
FROM (SELECT *
FROM Tabs
WHERE Tabs.PortalID = 4) T1, TabModules T2
WHERE T1.TabID = T2.TabID
ROLLBACK TRANSACTION
I hope it helps,
Val