why are local file transfers slower than 1Gbps /100Mbps

For the first part of your question:

You are limited to the hard drive speed of your SLOWEST drive in the transfer. Your mega fast switch and NIC and badass new PC with the 15,000 rpm drives can only send data to the 10 yr old laptop as fast as it can write it to a drive.

For the second part:

It depends on how the devices are connected. If (as I suspect) your computers are on the same ip schema, and the switch has its uplink port into the router, then the router is not involved. The router would only be included if it were two pcs on different ip schemas or subnets.

There are quite a number of reasons this could happen. Not all hard drives are created equal and you would be lucky to get 1Gbps from a consumer drive except under ideal conditions such as reading a single, large file with no fragmentation. Lots of smaller files have added overhead, and fragmentation increases access time. Also, unless you have very expensive components, both the SATA and NIC require interaction from the CPU, so other programs will slows things down. If you are running anti-virus software this may also be checking the data as it is accessed further slowing down the process. Last, and this is probably least important, Cat6 is recommended for GigE.

One other minor point: Many routers and switches say that they're GigE capable, but are really just referring to the interface. Often the data transfer between ports will be limited to a much lower speed due to hardware/software reasons.