What version of routeros do you use?
What boot device do you use sata or usb ?
I have same hardware and can’t boot routeros from any disk.
System Freezes at loading system or crc error. http://forum.mikrotik.com/t/ros-not-working-on-ibm-server-from-3-5-any-news-on-3-18/25861/1
Hardware:
Supermicro X7SBL-LN1 Motherboard
2GB DDR2-800MHz ECC Kingston CL5 kit 2x1GB
Intel Quad-Core Xeon X3360 / 2.83 GHz processor
Intel PRO/1000 PT Dual Port Server Adapter (EXPI9402PTBLK)
With Ubuntu or vyatta boot without problem…