If you haven't done so already, I would recommend running the Validate & Repair tool on the data file from the File menu > File Operations > Validate & Repair option.
In the Validate File window that opens, click the top box to "validate file" and then click OK.
When the validation completes, a data log will open in Notepad, please let us know if any errors or issues are found/repaired, and when ready close and re-open Quicken.
After this process, are you still missing transactions?
Let us know!
-Quicken Tyka