I ran into that issue as well when beta-testing that release. In my case, I had a Publish module on the home page and had the articles/categories option "force display on page ..." selected. So Publish switches to the page being forced to (I'm not quite explaining it correctly, but hopefully that makes sense). What I did was remove all of the 'force display on' settings and reset them all to false using SQL:
DELETE FROM Publish_ItemVersionSettings WHERE ControlName = 'ArticleSettings' AND PropertyName='ForceDisplayOnPage'
DELETE FROM Publish_ItemVersionSettings WHERE ControlName = 'CategorySettings' AND PropertyName='ForceDisplayOnPage'
INSERT INTO Publish_ItemVersionSettings
SELECT iv.ItemVersionId,'ArticleSettings','ForceDisplayOnPage','False'
FROM Publish_ItemVersion iv
WHERE iv.ItemId IN (SELECT ItemId From Publish_Item WHERE ItemTypeId = 1)
INSERT INTO Publish_ItemVersionSettings
SELECT iv.ItemVersionId,'CategorySettings','ForceDisplayOnPage','False'
FROM Publish_CategoryVersion iv
WHERE iv.ItemId IN (SELECT ItemId From Publish_Item WHERE ItemTypeId = 3)
Also, make sure you upgrade to 5.3.1 after you upgrade to 5.3, as there are some annoying bugs in 5.3 that are fixed in 5.3.1.