Try turning off "automatically accept downloaded transactions" and see if you can change that before the new transaction is accepted into the register. Are the reminders executed to make register transactions before you download?
Where are the "Auto-accept downloaded transaction" settings?
There are two places where this is controlled in Quicken for Windows: - Globally, for all accounts, in Edit / Preferences / Downloaded Transactions - For each account individually, the global setting can be overridden from the Edit Account Details screen, Online Services Tab. Look for blue text "Automatic Entry is: ON / OFF". Click the text to change the setting.