When I first started wrestling with this question, I thought ranks worked in the manner you suggested: someone didn't "become" a general officer until the appointment had been confirmed by Congress.
Nagle's case, however, demonstrates that the commission is active with the appointment, and it's permanence is settled by confirmation.
As you pointed out, Eicher & Eicher state that his commission expired on March 4, 1863 (Civil War High Commands, 403). That is the date the 37th Congress adjourned sine die.
However, they returned the commission to the president without holding a confirmation vote close to three weeks previous, on Feb. 12, 1863 (Senate Exec. Journal, 37th Cong., 3d sess., February 12, 1863, 128).
Nagle's commission didn't expire then with Congressional rejection. It remained active until that Congress ceased to exist--in effect, a presidential recess appointment.
An officer appointed to the rank of general by the president when Congress is not in session is a general until that current Congress explicitly turns him down on their return or that Congress goes out of existence. (It's like the recent situation of Amb. John Bolton at the U.N.)
Some people find this sort of arcana boring. I suspect I'm not in that company here on this board. :)
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