Upgrade to 5.6.1 causing blocks to disappear, MySQL error

I am having trouble getting COncrete5 to upgrade to 5.6.1. I am getting the following MySQL error after running the script:

An Unexpected Error occurred while upgrading: mysql error: [1048: Column 'cID' cannot be null] in EXECUTE("INSERT INTO PagePermissionAssignments (cID,paID,pkID) VALUES (NULL,'728','1')")

I had advanced permissions on prior to the upgrade.

I also am experiencing issues with blocks disappearing on sub pages, and some blocks duplicating. I can roll back to with no issues and everything appear. to go back to normal.

Also, either I am missing something, or something dramatic changed. I used to be able to go into page types, select defaults, edit global areas, and update on child pages. Where did all that go? Clueless!!

I am definitely noticing a huge speed improvement on 5.6.1, but obviously have to deal with some fixes before I can roll it out.

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furehead replied on at Permalink Reply
I changed file
and added a check for missing cIDs... around line 680:

$permissions = $this->getPermissionsArray($row['cgPermissions']);
         $co = Page::getByID($row['cID']);
         if(empty($co->cID)) continue;

After that I was possible to upgrade to from