I'll take a wild guess at it -
The engine was shut down during the short circuit event, allowing the generator to slow down and stop under the short circuit, which mostly demagnetized the generator. With very little residual magnetism, it took several seconds for the generator to create enough voltage for it's exciter to produce enough current to run the main generator, resulting in no voltage out until you were able to run the engine for a while. Once it gets going again, it should re-magnetize and work OK.
You may need a way to manually "flash" the field (put some DC current thru the field to re-establish the residual magnetism).
Like I said - a wild guess.