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Why opening application with shortcut doesn't behave the same as opening it from the dock

I want to open an application (Zotero) with a shortcut in the same way it opens when I click on it in the dock. When I open it from the dock the application recalls the previous changes (window size, position etc.), but if I open it with a shortcut it gets rest to a default each time I use the shortcut. I have tried both Automator (Launch Application) and Keyboard Maestro (I have tried both Activate a Specific Application and Open Application).

Most puzzling, if I try the run (Automator) or try (KB) function, the application opens as if clicked in the dock. Could someone explain to me what is happening?