In the Second Anglo-Dutch War Pepys found himself confronted by an unhappy General-at-Sea in Prince Rupert. I suspect Rupert considered himself an expert on victualing a fleet since he had previous experience of doing it on a zero budget:
In August 1648, Sir Robert Rich, 2nd Earl of Warwick confronted a Royalist fleet commanded by Prince Charles in the shallow waters of the Thames estuary. Charles sailed back to Holland, with Warwick in pursuit, who blockaded the Royalists in the neutral Dutch port of Helvoetsluys, where Prince Rupert took over command.
Unable to attack in neutral waters, Warwick maintained the blockade for several months, during which four of the Royalist ships defected back to Parliament.
Excerpted from Rupert, Prince Palatine -- by EVA SCOTT
Late Scholar of Somerville College, Oxford
WESTMINSTER -- ARCHIBALD CONSTABLE & Co.
NEW YORK -- G. P. PUTNAM'S SONS
In 1648 the fleet was formally given over to Rupert's command. He reluctantly accepted, offering to serve nominally under James, Duke of York. Prince Charles insisted, and Rupert was invested "with all the command at sea that he formerly held on shore."
 Warburton, III. p. 257.
The facility with which the exiled Cavaliers took to the sea is strange to modern ideas, but in the 17th century the line between soldier and sailor was not finely drawn. In Rupert's case his education among the amphibious Hollanders probably stood him in good stead. He seems to have thoroughly understood all nautical matters, and on one occasion we read: "By the ill-conning of the mates the ship was brought to leeward, which caused the Prince to conn her himself_."
 Warburton, III. p. 386.
Some of Rupert's friends tried to dissuaded him from "an undertaking of so desperate an appearance," but he was determined to do his best, and Prince Charles frankly acknowledged that, but for his cousin's "industry and address" there would have been no fleet at all.
 Warburton, III. P. 255.
 Transcripts. Charles II to Rupert, 20 Jan. 1649.
Chancellor Hyde, who never loved Rupert, wrote to Sir Richard Fanshawe that the preservation of the fleet must be entirely ascribed to the Prince, "who, seriously, hath expressed greater dexterity and temper in it than you can imagine. I know there is, and will be, much prejudice to the service by his being engaged in that command, but the truth is there is an unavoidable necessity for it."
After recounting the bad behavior of Capt. William Batten and Capt. Jordan, who had corrupted the sailors, and refused to put to sea, Hyde adds: "In this distress Prince Rupert took the charge, and with unrivaled pains and toil, put all things in reasonable order. ... And really I believe that he will behave himself so well in it that nobody will have cause to regret it."
 Clar. St. Papers. Chancellor Edward Hyde to Fanshawe, 21 Jan. 1649.
And Rupert did behave well. No undertaking was too arduous or dangerous. His tasks were so varied it seems scarcely credible they were performed by one man. He became a merchant; he discussed the prices of sugar, indigo, tobacco, and other commodities, and personally conducted the sale of his prizes. He attended to his own commissariat; dispensing with the cheating commissioners, as "unuseful evils."
 Warburton, III. p. 295.
Rupert gravely considering the quality of "pickled meat," or lamenting that peas and groats are both too dear to buy.
 Rupert Transcripts. Chancellor Edward Hyde to Rupert, Dec. 11, 1648. Hermes to Rupert, Jan. 12, 1649.
"Concerning the pork, he tells me he doth not think there can be so great a quantity provided suddenly," says a correspondent. "He hath not yet provided any shirts nor apparel for the men."
 Rupert Transcripts. Ball to Rupert, 15 Dec. 1648.
Rupert was his own recruiting officer, and went from port to port in Ireland, persuading men to join his fleet. He was overwhelmed with administrative correspondence from his officers.
Mutiny was frequent; Rupert's presence usually quelled it.
While the fleet was at Helvoetsluys, there arose some discontent in the "Antelope," beginning with "a complaint upon victuals."
Rupert went on board, and promptly told the men that they were free to leave the service.
To this they made no answer, but they were unappeased, and when, two days later, Rupert sent for 20 of them to help to rig his own ship, they refused to come.
Prince Rupert then went again to the "Antelope," and "walked the deck, to see his commands obeyed." The sailors crowded about him, and one had the courage to shout a defiance. His example could have inspired the rest, so Rupert acted with extraordinary promptitude.
Seizing the mutineer in his arms, Rupert held him as though about to drop him over the side, which "wrought such a terror upon the rest, that they forthwith returned to their duty."
 Warburton, III. pp. 262-264.
There frequently was no money to pay the sailors, so mutiny was to be expected. Nominally the men were paid 25s a month, but, unless prizes were taken, they did not get the money. Usually they acquiesced to the obvious with admirable resignation.
But in 1648, five sailors went from Helvoetsluys to Prince Charles at The Hague with a request to be told whether he had any money or not. Being truthfully answered that he had none, they expressed themselves satisfied with a promise of shares in the next prizes, and returned to the fleet, having, as Chancellor Hyde informed Rupert, "behaved themselves very civilly."
 Rupert Transcripts. Chancellor Edward Hyde to Rupert, Jan. 1649.
And not only for money to pay his sailors, but for every other necessary for three years Prince Charles was dependent on the prizes taken by Rupert. "Being totally destitute of means, we intend to provide for the satisfaction of our debts out of the proceeds of the goods in the ship lately taken," he wrote in 1650.
 Warburton. III. p. 308. Charles II to Rupert, Jan. 27, 1650.
While the fleet lay inactive in 1648, Prince Charles was engaged in negotiations with the Scots.
So Rupert probably considered Pepys another one of those "cheating commissioners" and an "unuseful evil."
Ah-ha ... I had forgotten this incident where Pepys reveals feelings about Rupert in 1660:
'... it was late in September, 1660 when he [PRINCE RUPERT] arrived in London.
'Prince Rupert’s coming had been for some time anxiously expected, although he was evidently regarded as still in the Emperor's service. "For ambassadors," it was said, "we look for Don Luis de Haro's brother from Spain, with 300 followers; Prince Rupert, with a great train from the Emperor; and the Duc d'Epernon from France, with no less State."
 Hist. MSS. Com. Rept. V. App. I. p. 173. Sutherland MSS., 4 Aug. 1660.
'Rupert came in a strictly private capacity. On September 29, 1660, Pepys recorded in his diary: "Prince Rupert is come to Court, welcome to nobody!"
 Pepys Diary, Sept. 29, 1660.'
Why 'Prince Rupert had, this early, incurred the diarist's enmity is puzzling. Later, the causes of it are perfectly understandable. Although unwelcome to Pepys, Rupert was welcome to many people, and not least so to the Royal family, who received him as one of themselves.'
I can find no mention of Rupert carousing through Huntington, or visiting Hinchingbrooke, or even Cambridge, during the Civil Wars ... but maybe Pepys had heard bad things? I can't think of where Rupert and Admiral Montagu could have met before the Restoration. It's very odd, but here it is. The seeds of enmity were sown before 1660.
Lightly edited from “Rupert, Prince Palatine”
by EVA SCOTT -- Late Scholar of Somerville College, Oxford
WESTMINSTER -- ARCHIBALD CONSTABLE & Co.
NEW YORK -- G. P. PUTNAM'S SONS
Chart showing the number of references in each month of the diary’s entries.