As captain of the Inconstant, Shepherd was involved with securing deserted vessels near San Francisco in 1849. At that time, he was in charge of 360 seamen and 55 marines. Deserting was a difficult problem when crews reached shore, one which Shepherd also faced when one of his crew died and the rest went to shore to bury his body (one member deserted under the guise of finding a stone for the burial). To that effect, Captain Shepherd decided to place sentinels with loaded muskets on deck with orders to shoot at any seaman seen as trying to escape. On one occasion, the captain had to order fire upon a man who jumped overboard, but he was later obtained by officers who chased after him in a smaller boat, and was subsequently punished. Amidst the upheaval, another man was found to be missing; it was later determined that he had jumped overboard about the same time as the first man and had escaped.
Under Shepherd’s command, the Inconstant also sailed around South America. During his voyages there, as part of his duties, he hosted at least one prominent colonial governor, which involved firing a seventeen-gun salute. Though he was described as disciplined, he displayed his sense of humour and diplomacy in one particular instance: Shepherd withheld the firing of the guns and simply made a silent show of it, as he had previously been requested by the Governor to cease fire when conducting target practice, as his herd of cattle was frightened of the noise. Captain Shepherd fired the guns as the Governor left, pleasing him greatly, and thereby affording his crew the ability to conduct target practice from then on.