Core 6.2.x is maintaining backward compatibility with Agent versions 6.x and 5.4.3. Anything older than 5.4.3 will be automatically paused.
In order to resolve the paused state, agent software must be upgraded. Please note that Server 2003 support has ended in 2015 and it's no longer a supported OS. Attempts to protect servers running 2003 from 6.2.x Core will generate error: "Not found" even though it may have agent 5.4.3 up and running.
As a workaround: Server 2003, if running on a Virtual Machine, can be protected agentlessly.