There is an answer to a similar problem in the Quicken Community. It might be partially right since I downloaded and then deleted three of the four months I was trying to upload. It doesn't explain way January would not show up.
Read below:
Quicken isn't recognizing them because it sees them the second time as a duplicate of a transaction that it has already seen (the 1800) and it has. The originals were the ones you deleted.
One way around that is to download into a new temporary account, accept the ones you need and then move them to the original account. When you are done with that, delete the temporary account. The next time you do the QFX download, Quicken will recognize any dups and not show them and only present the new transactions.
If you have a recent backup, you could restore it and you will find that you second downloaded QFX file should be imported and displayed in the downloaded transaction area.