I have NEVER seen a damaged network cable "slightly reduce the throughput" especially in a scenario such as this, if you've got a broken cable the chances are it'll just not work or be very very slow... (bits per second) Even if you have a semi broken cable udld usually detects it and stops it from forming a link.
I don't quite understand how standing on a cable makes it not conform to Cat5E standard? the 5E simply means that it uses all 4 pairs (1000base T4) so it can support short run gigabit, if you stand on the cable does this mean the other 2 pairs cease to work?
Also QOS isn't going to make any real difference as its not a multilayer switch, and can only do 802.1p TOS classification, it has 4 queues and will only start dropping frames when the queues start getting to 75% full. Again, not enough traffic for this to make a difference.
It could quite possibly be a duplex mismatch on the switch or one of the PCs but again I suspect that you wouldn't even get close to 100Mbit with a duplex mismatch.
I'd seriously say its something to do with one of the pcs or hard disk limitation or a duplex mismatch..
I give up lol