There are many things to consider when using any tcp app for determinig throughput. Things such as TCP window sizes, acks and other settings come into play. Especially the TCP window sizes. These will all affect data transfer rates. File tranfers and most other forms of TCP communication are poor tools for determining performance of the hardware.
There are some free tools out there for determining optimum tcp window sizes and other values.
My guess would be that for file transfer between pc's on the same switch, you could set the tcp window sizes to their max and be fine, but you should do due diligence and research.
I have often had to adjust TCP settings to get max throughput for data replication apps. I am sure there are lots of documents out there concerning the topic.