are you pointing to the console version of the macro? in other words if you perform "SYST:SHORT<n>:PATH?" query, where <n> is the macro number you picked, what do you get? in my example if I perform that query I get "C:\Program Files\Agilent\Network Analyzer\Applications\CharacterizeAdaptorConsole\AdaptorCharConsole.exe".
the none console version of the macro "CharacterizeAdaptor.exe" does not take any command line arguments and if your shortcut is pointing to it, then that is why it just pops up and sits there.
Mine is also pointed to C:\Program Files\Agilent\Network Analyzer\Applications\CharacterizeAdaptorConsole. I also opened a cmd box and changed directory to there and ran CharacterizeAdaptorConsole with the argument string both with and without full path names for the directories.
Finally I did a search on C drive for another instance of CharacterizeAdaptorConsole.exe. Didn't find any other instances. Is there any way to ensure that I have the correct version of CharacterizeAdaptorConsole?