OK. A summary to the best of my ability from the words of Commander Bruce Nicolls. Sorry about the delay; I have been trying unsuccessfully to post this reply since Sunday morning.
There are some who claim the name Union Jack should only be used when the flag is flying from the bows of HM ships, but this is a modern view, not supported by the historical facts. When the British flag was introduced in 1606 for use at sea, it was flown from the main masthead, but by 1627 it had become the custom to fly a smaller version of the national flag from the mast on the bowsprit. Then, the word jack could mean small, as it still can today, and the smaller flag was called a jack. That does not preclude the word jack being used otherwise than to mean small. Although the flag has never been adopted as the national flag, it became used as such and the name Union Jack was given in Royal Proclamations and Admiralty Instructions. In 1902, after the design of the flag had been formalised, the Admiralty approved the general use of the term Union Jack. Parliament said in 1908 that �the Union Jack should be regarded as the national flag, and it may undoubtedly be flown on land by all His Majesty� subjects.�
I accept that disrespectful would have been a better word than insulting. The Union Jack has been proudly used by many people and has acquired its much respected name through four centuries of usage, which began earlier than the flags known as jacks. It really does not deserve to be demoted to just another flag.
Buckingham Palace say the name could come from the jacket worn by soldiers of the period, or from Jacobus or Jacques, referring to James I. These explanations may be doubtful, but they at least cast doubt on the modern view that the national emblem is a little flag flown on the bows of a ship.