Doesn't synchronize

You would not be able to upload some - but not all - of your files to the root directory of your server if the site definition was not defined properly so just go ahead and forget that wild goose chase right now.

Typically a folder (especially if there's a subdirectory where the updated content is being uploaded) will not update with current timestamp if only some of the content of the folder has been updated (again, content within a subdirectory of the folder).  For example: the wp-content/uploads folder's modified date is not the same timestamp as the most recent upload you made in wordpress because uploads are sent to wp-content/uploads/yyy/mmm/file. So in this example only the mmm folder name would mirror the most recent upload's timestamp that occurred within that respective folder.

Check inside the folder and ensure the newly-uploaded files are there... and they are! This is a non-issue false alarm. Just because the timestamp for the modified date of the folder is not recent does not necessarily mean the sky is falling and that the contents of the folder are not being uploaded. Open the folder and you'll see recent uploads with modified timestamp more recent than the parent folder's modified timestamp.