Take a look in Tools>Online Center, Transactions tab to see if any pending transactions show up in the problem accounts.
In Preferences, do you have Sync turned on or Off. If On and you do not use the feature, Reset the cloud file without syncing first and then turn the feature off.
If Online Billers are set up in any of these problem accounts, make sure pending bill payments are not the source of the flag.
You said you turned off auto updates, did you mean Auto Accept? If not, turn off Auto Accept in Account Details for the account and see if the flagged transaction appears in the Compare to Register window, Downloaded Transactions tab in the problem account register.
Are you running the latest version of Quicken? For a while, Quicken was experimenting with downloading pending transactions and those would appear as phantom red flags. The latest version does not have that issue.
Try toggling the auto-entry option to ON. then check the register to see if it is there. If so delete it. Since it may be old, you might have to scroll back in time to see it. Then go back and turn auto-accept off.