Here is a thought: If the problem is only on MSWin32 machines, then wrap that bit of Win32 specific code into a block that only gets run on Win32:

if( 'MSWin32' eq $^O )
{
    require Win32::GUI;
    # Win32::GUI->import(); # Pretend to be 'use' ???
    my ($DOS) = Win32::GUI::GetPerlWindow();
    Win32::GUI::Hide($DOS);
}
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Or something like that.