Checks not clearing

Are these paper checks which you wrote and mailed yourself?
Are the check numbers 4-digit, 1234, or 5-digit, 10123?
How did these checks appear on your printed bank statement? "Check 1234" or similar?

For best results I always recommend that you record each paper check at the time you write (or print using Quicken) and mail each check. That gives you a correctly defined register transaction with a proper Payee Name, Category, Memo, as you need it. What's downloaded from the bank does not have any of that detail.

Are you automatically accepting downloaded transactions into your registers?
If so, I recommend you turn off the "automatically accept downloaded transactions into registers" setting to gain better control over what is downloaded and what to do with it. It's quite possible that Quicken mismatched the downloaded check transaction to a prior transaction of the same amount instead of creating a new register transaction … that makes it appear as if the "transaction did not 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.