The config firmware / OS versions mentioned are known to work well. Interestingly, it appears your issue was only experienced with ESXi 6.0 and not with ESXi 5.5. (In general this makes me think that this problem is not with your config, but that particular OS release).
However, Specifically you state that you are running Cisco custom image of ESXi 6.0 U2. This version has been tested by Cisco and Nimble for dual path connectivity.
Let me ask a few clarifying questions:
1) Any chance you actually installed ESXi 6.0_U1? I ask as the U1 version has a known problem with some later model B200 M4s. Reference Cisco's HCL http://www.cisco.com/web/techdoc/ucs/interoperability/matrix/matrix.html)
2) Out of curiosity, did you initially install the ESXi host with a single path or with multiple paths?
3) Are you experiencing this issue on a single host or is it more systemic?
4) The UCS to MDS connectivity should be verified. FI-A and FI-B should be separate fabrics (each with it's own VSAN). If you have multiple uplinks with port channels, verify the MDS upstream switch config matches.
5) Verify the UCS boot policy. The primary connection should be pointing to the same interface on both Nimble Storage controllers (FC1.1 for example) The secondary connection should be pointing to the same interface on both Nimble Storage controllers (FC 2.1 for example). It should look something like this: http://www.cisco.com/c/dam/en/us/td/docs/unified_computing/ucs/UCS_CVDs/smartstack_cs700.docx/_jcr_content/renditions/sm…
If nothing obvious comes from these questions, then I would suggest engaging Nimble Storage support to do a through review of your environment.