Found in the 5.0.3 agent product guild PDF, that the new command should be
/Library/McAfee/cma/bin/msaconfig -custom -prop4 "String"
But that's still not working. No errors, but according to "cmdagent -i", it's not set.
So it turns out I'm supposed to use the "maconfig" command now, not the "msaconfig" command. I missed that bit. All good now, things are back to working!