I have a 1GB fiber connection into a media converter, about 3 feet of CAT6 into eth1 of the CRS109
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In this one that I am having issues with There are checks beside 10M half, 10M full, 100M half, 100M full, but the 1000M and higher speeds do not have checks beside them. This means that the ISP node is not advertising the 1GB speed correct?
No, as you are not connecting directly to the ISP node you cannot tell what it is set to.
is there anything else that could be causing this?
The media converter, the Mikrotik is showing what the converter is advertising on its copper port.
Once that has been resolved if you are using the CRS for routing you won't get anything like 1Gbps, they are designed wire-speed switches with routing/firewallling limited by the performance of the CPU - it is the same specification as a RB2011.