This was a period of severe unrest, political upheaval, civil war and revolution in Britain and Ireland.
It may have been something to do with James II and Tyrconnel's repression of protestant landowners, businesses, government officials, army control etc - there was widespread fear of sectarian massacre and many protestants fled to England, Wales and the Isle of Man.
William (III) of Orange's invasion of Ireland - perhaps a number of Manx residents joined Schomberg's army in 1689 or William's in 1690 and fought at the Boyne, settled conquered lands or returned to their Irish businesses and lands - the Isle of Man has been a favoured destination for Irish refugees since the Iron Age.