I assume the HP and Linux machines are on different VLANs since you stated there's no extended access-lists applied. 6500 switches should have MLS enabled by default unless someone manually turned it off. With MLS packets between devices connected to the same switch should be switched even faster.
The possible causes for low throughput in your scenario can be errors on switchport, incorrect duplex settings between the switch and client, ftp application, busy switch (high CPU utilization) etc. Check the ports to which the devices are connected for errors, hardcode the duplex to full (if possible) on both the switchport and servers itself, check the CPU utilization of the switch itself. If none of that is an issue try a different application and see if that helps.
We are pleased to announce availability of Beta software for 16.6.3. 16.6.3 will be the second rebuild on the 16.6 release train targeted towards Catalyst 9500/9400/9300/3850/3650 switching platforms. We are looking for early feedback from custome...