Scorbutus was again a problem on Logan's voyage on the Fanny in 1832. However on this voyage he had far more to worry about. An outbreak of cholera, attributed by Logan to a last minute drunken sailor from Blackwall, raged through the already debilitated female convict population, before the Fanny had even departed England's shores.  An additional surgeon, William Marshall of the HMS India was placed on board in case the outbreak could not be contained. Many women became ill, six dying before the disease eased its grip.  The women, already weakened were then susceptible to scurvy and the surgeons had the problem of being unable to administer nitre to combat complications from scurvy as the women could not keep it down. The surgeons insisted on putting into the Cape where fresh provisions were found for the women. This assisted in their recovery however unexplained fevers also broke out on the ship. Logan attributed them to the ship having been too near the coast of Africa and later after leaving the Cape, to the effects of the cold damp atmosphere. In fact dysentery was the cause of much grief on board the convict ships. The close conditions and appalling sanitary treatment ensured that dysentery was rife. Sometimes there were no water closets. On the Champion the water closets were installed however they leaked throughout the entire journey leaving the convicts in damp unhealthy conditions for all of that time.

By the time Francis Logan sailed with the Royal Sovereign in 1835, he was well experienced in many of the problems that would beset them on this voyage however the sheer number of illnesses may have overwhelmed him on this occasion. John Davidson Barnes a surgeon attached to the 17^th or 28^th Regiments was also on board although he  seems only to have assisted in the post mortem of Samuel Knight who died of an aneurism even before  the Royal Sovereign set sail. There were the usual illnesses such as rheumatism, whitlow, catarrh, phthisis, abscess and epilepsy to deal with. However scorbutus was to be suffered by no less than 44 of the convicts and soldiers on board. As the authorities had not listened to Logan’s recommendation back in 1825 he decided this time to conduct an experiment of his own to test his theory of cayenne and garlic (or any of the Capsicums) as a cure for scurvy.  He could only do this on a small scale, as he had to beg the cayenne from the ship's Captain Mr. Moncreiff who was  unwilling to part with too much. However Logan found that the patients he had treated with the cayenne had suffered less with the scurvy than those he had not, and he again recommended the use of alternatives to lime juice.

Logan seems to have attended to the convicts and soldiers alike in a caring manner. He treated 13-year-old William Bailey for catarrh (a cold) and several convicts and soldiers consulted him on more than one occasion. He nursed several Patients back to health. Twenty eight year old John Carrigan, one of thirty-two soldiers of the 17^th and 28^th Regiments on board however was not so lucky. He died apparently from the effects of scorbutus after many days of illness and care by Logan.  John Charlewood was more fortunate. He made it to Sydney however Logan states that he would not have survived another two days at sea. He was forwarded immediately to the General Hospital in Sydney.

Francis Logan left the Royal Navy in 1841. He was born in 1780 in Ayreshire, Scotland and undertook medical studies at Glasgow University in 1804. He had joined the Royal Navy after 1806 and married Janet Wallace in 1837 when he was 57 years old. Their son Houston Francis was born in 1838. They traveled to New Zealand on the Bengal Merchant in 1840 and Logan was Surgeon Superintendent on this voyage. He was also described as a naturalist. Francis Logan died in 1862 in Wellington, New Zealand aged 84. His wife Janet lived until 1903.