Actually, it was quite a controversial issue in its day, as the settlement of the border was driven by the Klondike Gold Rush and the other gold rushes that brought tens of thousands of people to Alaska and the Yukon, with millions of dollars at stake.
Stuart Tompkins' 1945 paper, "Alaska's Boundaries" in Canadian Historical Review is one of the pioneering papers with regard to the history of the boundary, but boundary issues show up repeatedly in popular histories of Alaska, such as Haycox's, Borneman's and the textbook written by Naske and Slotnik.
First, though, you need to understand the state of borders in the early 19th century. The United States, Great Britain, the Spanish Empire and the Russian Empire all had overlapping claims on the Pacific Northwest, including Alaska. The Napoleonic wars and the War of 1812 had prevented any side from making a concrete and irrefutable claim on the region, but after those wars concluded, there was great interest in settling the unsettled situation.
The Spanish were the first to withdraw from their claims, with the Transcontinental Treaty between Spain and the United States. This left the British, Americans and Russians.
American-Russian relations were good from the founding of the United States right up until the Bolshevik Revolution. Both the United States and Russia saw each other as a counterweight in global politics to Britain's overweening power. As their interests tended to coincide, and they had few areas of conflict, they maintained good relations.
This was the case in the Pacific Northwest. Tripartite negotiations began in 1822, but they moved slowly, partially because the talks had to switch locations from Washington, D.C. to St. Petersburg, Russia. When the British proved intransigent, the Russians and Americans neatly outflanked them in 1824 by signing a dual agreement recognizing the other's boundaries at much the same place they are today. This left the British in a much more difficult negotiating position.
Though the British and Americans were unable to come to an agreement (the American-Canadian border would not be settled until the Oregon Treaty of 1849), the Russians and British did reach an agreement. The 1825 Anglo-Russian Convention ratified the southern border of Alaska at 54°40′ North (the same as in the American-Russian agreement) and set the boundary of Russian America at longitude 141° West, with the exception of a listiere along the Pacific Coast to the southern border.
When it came to defining the eastern boundary of that listiere, the treaty said that "the line of demarcation shall follow the summit of the mountains situated parallel to the Coast, as far as the point of intersection of the 141st Degree of West Longitude (of the same Meridian); and, finally, from the said point of intersection, the said Meridian Line of the 141st Degree, in its prolongation as far as the Frozen Ocean ..."
The treaty also stated that if the mountains along the coast were more than 10 leagues from the shoreline, then the border would stretch along that 10-league line instead of the summits.
If these boundaries seem vague to modern eyes, they definitely are. They're also very typical of treaty boundaries in an era when the terrain was not completely surveyed. Very little cartographical information beyond the coastline of Alaska was available to Europeans at this point. A similar situation arose in 1783 when the United States set a border with British Canada that ultimately had to be fixed with the Convention of 1818, but that's a separate issue entirely.
In any event, the boundaries set in 1824 and 1825 largely stood unchanged until 1900, though not without occasional incident. The Anglo-Russian Convention was supposed to allow British access to northern British Columbia via rivers running through Russian America, but different interpretations of that access led to the Dryad affair of 1834 between the Hudson's Bay Company and the Russian-American Company. That affair was settled amicably when the HBC agreed to lease the mainland portions of the listiere from the RAC in exchange for supplies given to the Russian traders.
Even after the Alaska Purchase of 1867, there were few problems with the boundaries set in the 1820s. One of the biggest issues arose in the late 1880s when Canadian and British whaling vessels began intercepting fur seals bound for the Pribilof Islands west of mainland Alaska. Sealing was extraordinarily regulated by the standards of the time in order to preserve the population of fur seals for harvest, and disputes over the right of Canadian and British ships to hunt seals offshore led to the American seizure of several vessels and a diplomatic controversy.
This controversy was settled with a diplomatic convention mediated by the French, Swedes and Italians, who found the British within their rights. The continued hunting would not be curtailed until a second convention in 1911. There were also minor territorial squabbles: the Canadians who began laying out a town, only to be told they were in the United States; a trader who unloaded his goods onto territory he thought was Canadian but was American, and so forth.
It was the Klondike Gold Rush that brought unavoidable controversy. During negotiations to obtain 54°40′ North as the southern border of Alaska, the Russians had agreed to move the eastern border of Russian America 2° west, from 139° West to 141° West.
On Aug. 16, 1896, at 64°02′31″ North, 139°25′20″ West, gold was found in huge quantities along Rabbit Creek, a tributary of the Klondike River. The Juneau gold rush had already brought thousands of people to the listiere region, and smaller gold rushes had brought miners to the Fortymile River region along the border and along the Yukon River, but this rush dwarfed them all, pulling tens of thousands of people to the far north from around the world.
To get to the area, they were almost required to cross American territory (there was an all-Canadian route to the Klondike, but it was so treacherous that it's memorable only for the horrific slog that it was). The Northwest Mounted Police were a stabilizing presence both at the border and within the Yukon, and Dominion surveyor William Ogilvie was already in the territory, marking a tentative U.S.-Canada line, but the Americans were slower off the start. In 1899, with the British (Canadians) already in control, American Secretary of State John Hay agreed to a modus vivendi until the issue could be settled.
When the Americans were ready to settle, they came in full-bore. With Theodore Roosevelt as President, they could hardly do otherwise. This was the peak of Manifest Destiny thought, and American triumphs in the Philippines and Panama would soon be followed by one in Canada, Roosevelt believed. Thomas Bailey discusses this in his Diplomatic History of the American People.
The issue was the vagueness of the 1825 border, which presupposed a continuous line of mountains paralleling the coast. The mountains neither paralleled the coast nor were continuous, something revealed by better maps. British Columbians, Britons and Americans each had differing interpretations of the 1825 boundary line, something helpfully illustrated by a Wikipedian clearing up an early 20th century map.
Roosevelt disdained the idea of a convention to settle the dispute, but he nonetheless agreed to the 1903 Hay-Hebert Treaty, which called for the appointment of six commissioners to settle the border. Three commissioners were to be American, two were to be Canadian, and one was to be British. In that year, the commissioners met in London and came to an agreement that resulted in our modern border. The event was a tumultuous one for Canadians, who felt betrayed when the British commissioner voted along with the Americans on a compromise line that tended to favor the American agenda.
The Canadians (correctly) believed that the British commissioner had gone along with the Americans to smooth British-American relations, but with the benefit of hindsight, we can see that there was little chance of the Canadian viewpoint coming out on top. Roosevelt organized a bellicose and aggressive campaign to get a pro-American line, and as he told the commissioners: "You will impartially judge the questions that come before you for decision," but "in the principle involved there will of course be no compromise." (This quote comes from an written by Bailey in 1937 in Canadian Historical Review)
Though Roosevelt didn't want to compromise, American and Canadian boundary disputes continue to be resolved by that principle. There are many even today, particularly over fishing. Dwindling returns of salmon in some runs have put strain on the Pacific Salmon Treaty at times, with people on both sides of the border unhappy. Transboundary gold mining by international firms on the Canadian side of the border (but upriver of American rivers) has also raised environmental concerns, particularly after the Mount Polley mine disaster.