If the torrent archiver or its container suffers a crash, downloads will probably continue (via Azureus) on next startup, however no TorrentDownloadListener instances will be attached to them. Therefore no "download complete" messages will be sent to the notification system.
The fix should probably go into:
uk.org.microbase.resource.torrent.archive.ws.TorrentArchiveServiceImpl
After starting Azureus and the Microbase plugin, scan for all non-complete downloads, and attach listeners. This should probably be done before event log initialisation.
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This has been fixed for a while.