if your data is encrypted, your isp cant see its contents so they wont suspect torrents. also, if its one outbound connection, that doesnt look like a torrent to an isp.
did they mention how they narrowed it down to a network problem?
does it take a long time for the connection to drop or does it happen after a few minutes? if its a short amount of time, you could try running a datacapture to see what packets are making it to their destionation and what happens when the connection gets interrupted. you can also try running a traceroute to your destination and then run one right after the connection drops. while the traceroute wont "prove" anything, you can see if your connection was going via LA one minute and then the next minute its going via NY. you can also try running a constant ping to your destination and try to correlate any abnormalities with that ping to drops in your backup, however your backup provider may not like that so make sure to get clearance from them before sending a whole bunch of pings at them.
does this disconnect happen at all times of day? its possible that your isp does routine maintenance at the time that you normally run your backups (i.e. at night) which would cause your connection to be interrupted.
basically, what im getting at is that internet is never a reliable connection so any interruptions (hardware failure, routing changes for whatever reason, congestion) may produce unexpected results.
and one more thought....i dont know the best way to check this but can you run some streaming media for extended periods of time without any interruption? maybe its just the length of the connection. try asking your isp to see if there's any max length of a connection before it gets reset.