I opened my account a few days ago and it just finished syncing. I am still missing most of my Xbox One games; everything older than the past 2 weeks is not there. Not sure if this is normal, I've unselected and re-selected the "Sync Xbox one and Windows Games" option a few times.
The site takes about 24-48 hours for your Xbox Live account to be synced and can take up to the first seven days after a new account is added to fully process every game you've played, especially if you've played a large number of them.
Looks like you still have some achievements queued up to sync, so let the cycle run another few days and let me know if it still looks off. I can manually update if need be, but the system is set up to pace itself to avoid problems.