Freight money was a very important source of income for captains and flag officers on foreign stations, and as you say Anna, was available in peacetime as well as war. I believe the East Indies was a particularly lucrative station for freight money.
Prior to Nelson's lawsuit with St Vincent over prize money, he was also involved, along with other junior flag officers, in a dispute with him over freight money. In the end, Sir William Parker took legal action against St Vincent as a test case to prove the point that junior flag officers in the fleet were entitled to one third of the admiral's one third. This came up in the
thread on Nelson's lawsuit against St. Vincent. I think the distribution of freight money was not regulated by the Admiralty court, but was according to custom and practice, and thus more open to dispute.