It's hard to tell exactly what's happening and I'm not familiar with web querying in Excel, but my guess is RefreshAll isn't totally blocking so your code continues executing even if it's not done. In the second run the data has completed the refresh and

Win32::OLE->GetActiveObject('Excel.Application')

grabs the background Excel process you started previously, which now has all of the data. Since you're quitting anyways I would remove this (just create a new instance) and try sleep-ing for a few minutes after RefreshAll. You may need a while(1) loop that checks on the status of the data query, or set the BackgroundQuery property to 0 on every object (if that's the root problem).

Installing a signal handler to close and exit would also prevent Excel staying open in the background:

$SIG{INT} = sub { cleanup(); die "Caught interrupt"; };

... (main code) ...

cleanup();

sub cleanup {
  $Book->Save();  
  $Book->Close();
  $Excel->Quit();
}
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