Which Q product are you running, and what Release of that product? This info is at HELP, About Quicken.
By "update", do you mean a Q program update, or an update to your investment account(s)?
When you do TOOLS, Account List, what shows in the "Transaction Download", "Last Download" and "Financial Institution" columns adjacent to the account(s)?
What types of securities are generating these deposits? Stocks? Mutual funds? Are these the month-end payments on bond and money market funds?
Where are the T-Notes showing what you're seeing? Elaborate upon "lumped together". Graphics would be helpful.