It should be noted that your torrent client only updates with the tracker once every 30 minutes for each torrent. As such, there is a delay in your stats updating. On that note, with most torrent clients, when you close your torrent client or otherwise stop a torrent, any data that has been transferred since the last tracker update is generally lost. So closing and re-opening your torrent client is part of the problem.
As well, the stats on the site only show the total amount transferred for the current session. If for some reason you stop your torrent and restart it, the stats associated with that torrent on the site will reset back to zero until you transfer more.
Use of a VPN should not affect your stats at all, however if you use a proxy server on top of the VPN, this may explain the issue as proxies do not allow for proper traffic flow for new connections back to your system (among other reasons).