We did a test about measuring bandwidth of PCI-E 3.0 (x16) on SYS-7037A-i. Two Tesla K10 were installed into Slot 3 and 5, both slots were PCI-E 3.0(x16).
Slot3 seems lower than Slot5, it is a half performance via PCIe link. In other words, Slot3's performance was like PCI-E 2.0 (x16), not PCI-E 3.0 (x16).
Could you tell us some reasons about lower bandwidth of Slot3?
Please make sure the BIOS settings are Gen3 for both slots. If you set Slot3 to Gen2, it will have lower performance.