2510G Switches Sharing Single 1Gb Line To Servers But Internet Slow

About a week ago I changed over 9 HP Procurve switches that were previously stacking in series (yeah, daisy-chain) to a Access-Distribution type scenario with 2 (or 4 on server switches) Gb ports on each switch Trunked together connecting to a central full 48x Gb switch.

During this I updated firmwares on all the switches (most still on their shipped 5-8 year old versions) to the latest stable release (and in the process found out that HP switch firmware is absolutely brutal and untested - See ProCurve 2510G FW 11.16 as an example) .

I saw vast improvements across the network immediately after the change (wow, really? 9 48-port switches effectively sharing a single 1Gb line to the servers and internet was a bit slow? Don't tell my co-workers, they don't think that's possible ) .

The only thing that I didn't see an improvement in was on some Linux and BSD servers, which would top out at 11MB/s doing a SMB (SAMBA) transfer. These are managed systems part of our business system, but we still need to be able to pull local backups for ourselves. So I contacted our vendor. The vendor confirmed that the line speed is showing as 1000T-FDx (same as the switch is showing).

Vendor is now claiming that after these changes were put in place, the speed on their servers (and their servers ONLY) was reduced to a maximum of 5MB/s (~60Mb/s?) doing rsync transfers between themselves. And they are all on the same 2510 (48 port all 10/100/1000), which makes absolutely no sense whatsoever to me. Furthermore this is on the ONLY switch on the entire network that had an updated firmware already installed - that's not even a possibility here.

I put some windows servers on that switch and can get 60MB/s+ all day (SMB transfers). I've also tried from their one server that I can access to doing an rsync or scp to another BSD box, and max out at 15MB/s (with 100% CPU usage on the test box - I'm assuming the decryption is pretty heavy?)There is absolutely no QoS, limiting, or any possibility of throttling the links the servers are on the switch. There are no excessive broadcasts saturating it, and the ports and cables test fine.