If a switch is used with autodetect it can easily fail to configure duplex (Full/Half) right.
If a Full Duplex system talks to a Half duplex system (Switch, or computer, it's about the endpoints on cables) then traffic will drop because of packet loss.
It can be identified on the FD side by checking counters, a lot of short frames, + crc errors are a hint in this direction. It might still work in one direction, (the file transfer that is) but not in the other direction.
A hub is allways Half Duplex, (hub != switch), configuring a FD interface on that is killing you connection but probably for a whole network segment.
Another problem might be a multi wire connection between a switch & system (channel agregation) if the switch has not been configured to use both interfaces as one channel then the switch will flap a lot between the interfaces.
Nice tool to check network performance is netio.
http://www.ars.de/ars/ars.nsf/docs/netio