In pursuance of an order of the Councell of State of the 5th of this instant May It is ordered that it be referred to the Comrs for the Navy forthwith to take care that such Standards, fflags and Jacke Colours for the ffleete be forthwith prepared as were in use before 1648 and that they be sent downe with all speed to Generall Mountagu as alsoe that Carvers and Painters be appointed to goe down for the altering of the Carved workes according to such directions as they shall receive from Comr Pett, who is ordered by ye Councell forthwth to goe to ye Generall. And the said Comrs are to give order for the sending downe to the Generall One silke Standard and one silke Ensigne and Jacke and such other silke fflags as may compleate a suite for the Naseby[187].
Instructions to this effect must have reached the fleet before it left England, but the flag-makers had evidently not had sufficient time to prepare the new royal standard, for on the 13th May, on the way over, (so Pepys, then secretary to Mountagu, tells us[188])
the tailors and painters were at work cutting out some pieces of yellow cloth into the fashion of a crown and C.R. and put it upon a fine sheet and that into the flag instead of the State's arms[189] which after dinner was finished and set up.... In the afternoon a Council of War only to acquaint them that the Harp must be taken out of all their flags, it being very offensive to the King.
The Union flag, like the Government, now reverted to its original form, but the right to fly it remained the special prerogative of the State's ships, a prerogative much sought after by merchant ships, and often assumed by them without warrant. For the next half century a long-drawn struggle was waged by the merchant shipping for the possession of this right. It begins with a special instruction sent by the Lord High Admiral, James Duke of York, to the Corporation of Trinity House on 9th March, 1661:
I desire you will give notice unto all Commanders and Masters of Shipping belonging to the Subjects of the King, my Sovereign Lord and Brother, that from henceforward they forbear to wear the Flag of Union; and also acquaint them, that such as presume to wear the said Flag contrary hereunto, the King's Ships will have orders to take it from them[190].
The Trinity House issued orders to this effect, but although the prohibition had been stiffened with a threat that the flag would be taken by force from those displaying it, the notices seem to have had so little effect that, on 19th Nov., when a royal proclamation was issued "For prohibiting the Imbezlement of His Majesties Stores," the opportunity was taken to make the further threat that the Commander of the ship would be seized also:
And for preventing the abuse which hath been of late practised concerning Flags, Pendents and other Ornaments His Majesty doth hereby strictly prohibit & forbid the use of His Majesties Colours in Merchant Ships, and doth Authorize and Command all Commanders and Officers of any His Majesties Ships of War not only to take from Merchants Ships all such Colours but likewise to seize the Commander of such Merchant Ships, wherein after the first day of April next they shall be used, and to bring them to condign punishment[191].
It is interesting to find here, as in 1634, an excuse made for the order which is not the main reason for it. No doubt a certain number of colours were embezzled and sold by the boatswains of the king's ships, just as the gunners embezzled and sold the powder, but the desire of the merchant shipping to fly the Union flag was not due to the fact that they might occasionally pick that flag up cheap, it was due rather to the privileges, especially freedom from pilotage and port dues in foreign ports, which the flag assured them.
Probably the further threat of imprisonment checked the practice for a time, but not entirely, for the Lord High Admiral was again taking action in 1666.
Warrant for taking into custody such Mars of Mercht Ships as shall presume to Wear the Kings Jack.