Is it a relatively new phenomenon? Given the importance of Scottish ministers historically in British politics, I was lead to believe that there was a time where Scotland was seen as truly British rather than a separate entity. If this was the case what caused the shift in opinion?
The History in this is based on being Scottish and it being taught a little in Scottish schools rather than a particular source.
Firstly, looking at the Act of Union is the wrong way to start. What you really want to look at is the 1705 Alien Act. In it's briefest form, it was a package of trade sanctions against Scotland which made the already bankrupt Scottish hierarchy have to submit to English Rule (as the Stuart dynasty had ended, England wanted to ensure that there could be no attempt at restoration as, in theory, the Stuarts could lay claim to the Scottish throne).
This link to the Scottish throne led to two uprising that we would call the Jacobite risings led by the Old Pretender James Francis Edward Stuart in 1715 and the Young Pretender Charles Edward Stuart in 1745.
The 15 was a case of the Highland clans being stirred, making small incursions into England, succumbing to superior numbers at the Battle of Preston and James Stuart being not very inspiring to troops. James "III" then went off to France where he stayed for the rest of his life.
The 45 is the altogether more interesting and romanticised of the uprisings. Britain was embroiled in the War of the Austrian Succession at the time and, as such, the troop presence on the mainland wasn't that big. At this point, Charles Stuart ("Bonnie Prince Charlie") landed and as able to raise 3,000 Highlanders. They fairly easily routed the British regiments in Scotland and invaded England getting as far as Derby before turning back (due to lack of support in England - it should be stated that they got this far without ever being in all that much danger. In fact, the decision to turn back was based on faulty intelligence that inflated the size of the British army opposing them). While getting back to the Highlands, the British Army beefed up by putting the Duke of Cumberland in charge and adding 5,000 Hessians. It meant the Jacobite force of about 7k would be facing off against a numerically superior foe and met at the Battle of Culloden. This battle was the last to be fought on British soil and was a rout of the Jacobites - they had no answer to the artillery on the field, resorting to sabre charges against cannon with inevitable results. Charles Stuart left the field in disgrace and hurried out of the country dressed as a woman. Never again would Scotland rise.
Scottish identity then took a hiatus. The armed opposition (in the Highlands) was crushed in the Highland Clearances which was an economic advance over a century in the making which changed how the tenancy and agricultural system of the Highlands was made up - the upshot was vast emigration to the Americas as the tactics used can only be compared to those used against American Indians (forcible relocations, burning houses down to force residents to leave) and is considered by some to have been a case of ethnic cleansing.
While there has been cultural romanticism (Sir Walter Scott and Robert Burns are the two go to writers for this - Burns, in particular, owing to his political views and revolutionary use of the Scots dialect in poems) it was crushed for a long time by economic pragmatism. Independence didn't have much support because it was economically impossible (North Sea Oil coming into the Scottish economy from the 1980s onwards has helped to destroy this perception). For example, the first devolution referendum in 1979 was defeated soundly whereas in 1997, after oil entered the equation, it was passed resoundingly.
So, the brief answer to this is that an organised Scottish independence movement lived for about 40 years post Act of Union - once the Stuarts had been defeated for good, the movement deflated due to the majority of Scots benefitting economically from Union combined with the fact that the biggest group of those who would have been pro-independence (the clans) saw their entire social system torn up and the population relocated or left to die. The independence movement revived in hearts due to a cultural revivalism in the mid-20th Century based around remembering Robert Burns and ably aided and assisted by the Scots revivalist poetry of Hugh MacDairmid (who is perhaps the most interesting poet ever to have lived, politically speaking). Once this cultural nationalism was revived an independence movement stuttered along, only gaining pace from the 1980's onwards when the economic argument behind independence became credible.
As a sidenote, what sort of effect did Irish independence have on Scottish nationalism?