Some programs can definitely affect speeds on your internet connection. Windows can be a major culprit as it downloads updates in the background without your knowledge and some of these can be quite large. Other programs like Antivirus and Firewalls can do automatic updates as well.
Peer-to-peer programs such as Limewire or Utorrent can constantly use bandwidth and if left sharing and unrestricted, can certainly cause speed issues.
It would be worth contacting support as we are able to see active connections that could be affecting your speed.
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