The FlexNet agent (and, I think, the SCCM agent) gathers the account name of the currently logged on user through the Win32_ComputerSystem.UserName WMI property on Windows. This property is collected by default; there is no need for special configuration. If you take a look at a .ndi file generated by the agent then you should see the value in there.
I wonder whether the problem you're experiencing is related to the observations made in the following recent discussion: Logged In User using FNMS Agent. In this discussion it was noted that it appears the 12.4 version of the FlexNet agent does not gather this data when running under the SYSTEM identity on Windows 10.
The Win32_LoggedOnUser.Antecedent property is a reference property to a WMI object. I'm not surprised to hear the agent fails to run in this case; I would restrict to properties referenced in the wmitrack.ini file to just simple-valued properties.
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