There's nothing to apologise for. I haven't properly documented the latest features yet.
All the FTP uploads (Data store, Webserver, Snapshots) are performed immediately after sampling, so they contain the latest data at the time of uploading.
Data store: the main stats are uploaded after every sample, the four per-tone zips are uploaded once an hour (i.e. the same timing as MDWS used to use).
Webserver: the frequency of the uploads is defined in the upload configuration.
Snapshots: all the local snapshots are processed according the Snapshots configuration, and if they're configured to be uploaded then this is done immediately after saving them locally. The way it works is that every snapshot is temporarily copied to an "Uploads" folder (including any manual snapshots which have been made since the last upload), then the entire contents of the Uploads folder is uploaded to daily folders on the server, and afterward the files are all deleted from the Uploads folder. The filenames of the uploaded snapshots are the same as the locally saved snapshots.