Normaly i get from my NAS easily 100MB/sec (it is only connected via a 1G Port).
After some time it drops to 10MB/sec.
Once i reboot the CRS312 it comes back to normal speed.
Im using 7.1.3 and the CPU temp is around 60degres Celsius.
All ports are set to switching only with L3 HW offload.
I have nearly every CRS3xx box in my network, but CRS312 is not one of them(yet!), but have not come across such issue.
Could you list your config. And double check your error counters on your connected ports/sfp’s to see if drops match against heat load( may be a sfp issue if you use them ? )
Other things you can try in the mean time is to downgrade to 6.49.3 Stable and don’t forget to update the System->RouterBOARD->Firmware to match your version of RouterOS