I am experiencing this same error when I attempt to run a Scan with the Endpoint Protection Cloud product, but this is using Server 2008.
After reading your other thread, andylee321, I was able to get the Server 2008 to register as a node in the Cloud Console (I had to install the KB update for TLS) but whether I trigger a Scan from the console, or manually on the system, it gives the same error above. It gets to the "File Scanning" portion, then abruptly stops.
I was looking at the documentation to run the Malwarebytes Breach Remediation Tool, like you mentioned, hoping to resolve this issue. But in the MBBR Guide that I have here, dated 30 October 2018, it states the tool only supports OS versions Server 2008 R2 64bit and above. My system is Server 2008 32bit... The tool that I have here is MBBRv2, dated 11/5/2018, file version 184.108.40.2065.
How did you get the MBBR tool to run successfully on Server 2003? Did you use an older version of this tool? Is that version still available for pre-2008R2 systems, such as mine?
Thanks in advance.