Usually when we see this type of behavior it has to do with the window spawning in an unexpected location, are you able to move the SMC window to see if the pop-up is behind it?
This SAS Note describes how to capture debug logging from SMC, which might be a good place to start:
Usage Note 43157: Capturing debugging messages from SAS® Management Console
https://support.sas.com/kb/43/157.html
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Greg Wootton | Principal Systems Technical Support Engineer