It isn't vSphere alerting, but the IBM server reporting up to vSphere. I'm guessing there is a setting in the BIOS that would cause the server to expect all four power supplies to be installed. I wouldn't expect an alarm from IPMI if the power supplies are not installed, only if they are installed and not connected and/or installed and failed. Please confirm this in the IBM server setup...
Do you have the blanks installed in the server where power supplies 3 and 4 would be located? I don't know whether IPMI logs this or not.