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I have a similar problem also with missing the "master password" prompt when Smartgit is minimized. There should be some notification to the user that Smartgit did not finish the operation and is requiring user attention.

What I do is e.g. try to push my latest changes, then minimize Smartgit to continue work on the next topic. After a while I check Smartgit again and notice that the push actually did not go through due to the "master password" prompt.