Program launching incorrectly when using a shortcut

When I try to launch my program with a shortcut or Process.Start it is running my if's saying that my files are missing and it is not launching the WPF windows. The picture below is what I am trying to launch via shortcut/process.start

if (!File.Exists(Environment.CurrentDirectory + "\\Multimanager.dll") && !File.Exists(Environment.CurrentDirectory + "\\Multimanager.dll"))
{
    MessageBox.Show("You are missing the 'Multimanager.dll' and the 'Updater.dll'. Please re-run the MMInstaller.exe to re-download these files", "Missing files", MessageBoxButton.OK, MessageBoxImage.Warning);
    Application.Current.Shutdown();
}
else if (!File.Exists(Environment.CurrentDirectory + "\\Multimanager.dll"))
{
    MessageBox.Show("You are missing the 'Multimanager.dll'. Please re-run the MMInstaller.exe to re-download these files", "Missing files", MessageBoxButton.OK, MessageBoxImage.Warning);
    Application.Current.Shutdown();
}
else if (!File.Exists(Environment.CurrentDirectory + "\\Updater.dll"))
{
    MessageBox.Show("You are missing the 'Updater.dll'. Please re-run the MMInstaller.exe to re-download these files", "Missing files", MessageBoxButton.OK, MessageBoxImage.Warning);
    Application.Current.Shutdown();
}
else
{
    string MMV = Multimanager.MMShared.version().ToString();
    string UV = Updater.UShared.version().ToString();

    var u = new Updater.UpdaterWPF(MMV);
    u.ShowDialog();

    var mm = new Multimanager.UUpdater(UV);
    mm.Show();
    u.Close();
}

Edit: If I launch the program manually with the .exe it opens fine