Secretary to the Royal African Company.
Sir Ellis (b. Elisha) Leighton (???-1684) was secretary to John Berkeley, 1st Baron Berkeley of Stratton when he was Lord-Lieutenant of Ireland in 1670 and British Ambassador to France in 1675. Elisha died on 9 January 1684 and his will mentions a daughter Mary. http://en.wikipedia.org/wiki/Alexander_Leighton
This man is hard to track down. Terry's link goes to his father, who does sound like an interesting character. His given name was Elisha, and I haven't found out when or why he changed it to Ellis. But more information can be found here:
LEIGHTON, Sir ELISHA (d. 1685), courtier; son of Alexander Leighton (1568-1649); colonel in the royalist army; joined royalist party abroad after Charles I's execution; appointed by Charles secretary for English affairs in Scotland, 1650; knighted, 1659; F.R.S., 1663-77; one of the secretaries of the prize office, 1664; LL.D. Cambridge, 1665; secretary to the lord-lieutenant of Ireland, 1670; recorder of Dublin, 1672.
---Dictionary of National Biography: Index and Epitome. S. Lee, 1906.
The real name of the Knight was Elisha Leighton, whose brother Robert, Bishop of Dumblane, became, soon afterwards, the excellent Archbishop of Glasgow, and as such is more generally known. Their father, Alexander Leighton, was a rank Puritan, author of Zion's Plea against Prelacy, for writing which he had his ears cut off, and was exposed in the pillory in that state, with his nose also slit. Elisha was apparently euphonized into Ellis by the courtier son, who is described by Le Neve as one of the Duke of York's servants. Pepys speaks of him as Secretary of the Prize Office, and adds, that he had been a mad, freaking fellow.
---Diary and correspondence of Samuel Pepys, the diary deciphered by J. Smith. 1854.
I'm surprised more of these Civil War veterans didn't experience temporary madness. The story on Leighton seems understandable:
During the civil war Elisha Leighton rose to be a colonel in the Royalist army.
After the battle of Worcester be escaped to Rotterdam with George Villiers, 2nd Duke of Buckingham in October 1651.
After fighting a duel with Major Nicholas Armorer in Brabant, in June 1652 Col. Leighton was sent by Buckingham to London with a sealed letter directed to Oliver Cromwell.
One account says the council of state refused to listen to Col. Leighton, gave him back the letter, and ordered him to leave the country. Elsewhere Leighton is reported to have had a two hours' interview with Cromwell, who ‘used him with more than ordinary courtesy’. (Both stories could be true.)
After Col. Elisha Leighton’s return to Antwerp he had a bad illness, became temporarily insane, and on his recovery turned Roman Catholic.
In June 1656 Leighton deserted Buckingham on the pretext that the duke did not ‘rightly submit to the king’. (He was right: By 1657 Buckingham had tired of his life in exile and returned to England. Convincing Oliver Cromwell that he was harmless, Buckingham won back his property by marrying the heiress of the man who held most of his lands - Lord Thomas Fairfax, late General of the Parliamentary forces.)
Col. Elisha Leighton subsequently became secretary to James, Duke of York, and was knighted at Brussels in April 1659. At the Restoration Sir Elisha Leighton made his peace with Buckingham, and was indebted to him for preferment.
Sir Elisha Leighton had a talent for mechanics, and became a F.R.S. on 9 Dec. 1663 … On 28 April 1664 Leighton was made one of the secretaries of the prize office (Cal. State Papers, Dom. 1663–4, p. 571).
For more information see https://en.wikisource.org/wiki/Leighton,_Elisha_(…
Chart showing the number of references in each month of the diary’s entries.