No matter what combination of auto negotiate or manual, and no matter what combination of advertised speeds, I have a few brand new board which have multiple ports that won't link at 1Gbps. Not with Cisco, not with Allied Telesyn, and not with other CCR1009's. I have tried 6.12, 6.15, 6.16rc with no change. Emailed supout's to Mikrotik with no response.

Over the last few years we had transitioned our entire network over to Allied Telesyn Layer 3 routers completely. They're fast and reliable. We wanted to come back to Mikrotik now that we see they have decent hardware with dual power supplies. But on our first $10,000+ order of equipment this is what we find. And with 0 support from the manufacturer. With Allied Telesyn we call, speak with someone, and within 24 hours would have a resolution or replacement.

So what is the problem here? Is his model another junker or can this be fixed?

Also Latest Routerboard firmware ?

Try and enable Flow Control Auto for TX and RX. Also enable it on the other side.

Make sure there are no STP or RapidSTP issues on the Cisco side.

Also, when upgrading the RouterOS version, make sure you also upgrade the firmware! You can do this at System --> Routerboard --> upgrade and then reboot after a little bit.

Personally I had no problems whatsoever linking stuff to the CCR1009. My RB2011 has also been solid since it was fixed.

I had this issue with connecting ESXI to my CCR. Solution was keep auto negotiate on but only advertise 1000m. Without this settings, I get half duplex 100m and other unwanted speeds.

You get some solution?