You are right, the 4900M is a Catalyst, not Nexus model.
I have figured out a different solution in the meantime: enable flow control (switch side)/disable pause frames (NIC side, ethtool) when connecting 82599EB controllers to the 3064. I would even argue the ixgbe driver must have a long-standing bug with pause frame autonegotiation, but of course, IANAE.
Thanks for posting.
Here are some solutions that may resolve your connection problem:
1. Update driver - you may download the latest driver here: Intel® Download Center
2. Advance Driver Settings that you may configure: Intel® Server Adapters — Advanced Driver Settings for Intel® Ethernet 10 Gigabit Server Adapters
I see you have enabled Flow Control. Try to disable other advanced features and observe your connection:
- Interrupt Moderation
- Interrupt Moderation Rate
- TCP Checksum Offload
Hope this is helpful.