Kirkby spent the fourteen months after his return without a ship to command, but was finally appointed to
HMS Southampton in 1694 and served in the Mediterranean under the command of
Edward Russell. The first signs of his aversion to fighting were noticeable in an engagement against two French vessels (the
Content and the
Trident) on 18–19 January 1695 off
Pantelleria. It was noticed that he: 'kept as far off' the heavily armed
Content 'as his guns could reach reasonably firing now and then 2 or 3 guns at him' He was consequently excluded from a share in the resulting prize money. Further problems were also apparent aboard the
Southampton. Her
chaplain, Ellis Cooper, left the ship after some unrecorded unpleasantness with Kirkby. Further punishments were meted out, the
boatswain was broken and flogged for disobedience and insolence, and a seaman was sentenced to be flogged and 'towed ashore' for 'scandalous actions'. The
Southampton, still with Kirkby in command, was then sent to the
West Indies in 1696, being present at the burning of
Petit-Goâve on 28 June 1697. Kirkby returned to England in 1698, where he was tried by court martial on charges of embezzlement and cruelty, accused of punishing a seaman for straggling by ordering him to be 'tied up by the right arm and left leg for several hours' The board cleared him, but Kirkby did not receive another command and spent the next two years without a ship and on half pay. Kirkby blamed this on 'the great power and interest of my Lord of Orford' (
Edward Russell). ==The West Indies, mutiny and court-martial==