There are no longer many disagreements of consequence over state boundaries' location. Most boundaries are settled, or 'cold' -- to use a term one occasionally sees (or used to). Among the unsettled or 'hot' boundaries there is Israel/Palestine, of course, which is something of a special case. There is the disputed India-China boundary, which has just recently flared up again (see also here). And there are, no doubt, a few others, e.g. the disputed India-Pakistan boundary in the Siachen glacier. (There are also, notably, disputes about islands but those necessarily involve maritime boundaries and are therefore in a different category.)
More common, I think, than disputes about location are disputes about a boundary's status. These disputes don't have to do with where the boundary is drawn but rather about the status of the territory it marks out. Take the cases of Abkhazia and South Ossetia, mentioned here. Supporters of Abkhazian independence presumably don't want a different location for the boundary marking out Abkhazia; rather, they want a change in the boundary's status, from a provincial to an international boundary. When an article about secessionist or independence movements refers to "the rigidity of boundaries," this distinction can get lost, because the reader may infer that a secessionist movement wants to change a boundary's location when it doesn't. The Balochistan independence movement, for example, would presumably be happy with the current location of the boundary marking out Balochistan as a province of Pakistan, but it wants the status of that boundary changed to an international boundary. (Note however that some cases, such as that of an independent Kurdistan were it to be achieved, might involve changes in boundaries' locations.)
Then there can be tensions and disagreements that involve boundaries in some way but are not about either the boundary's location or its status. Two states that share a boundary can disagree, for instance, over how to manage the movement of people and/or goods across it. There can also be violence along a boundary that doesn't, strictly speaking, have much to do with the boundary itself but is an expression of hostility between the countries involved that happens to erupt along the boundary for various reasons.
For instance, the recent clashes between Afghan and Pakistani soldiers along the Afghan-Pakistan border may not have much to do with the border itself. According to a May 2 NYT story (h/t FP's AfPak Daily Brief):
Afghan forces claimed on Thursday that they had overrun and destroyed a Pakistani-held border crossing in a remote area, an event that provoked a spontaneous outpouring of nationalist sentiment here, sending thousands of students into the streets to demonstrate and setting off lively debate on social networking sites. A funeral for Qasim Khan, an Afghan border policeman who was the only confirmed victim of the clash, turned into a patriotic rally.
The NYT piece goes on to note that the outcry over the death of one Afghan soldier at the hands of Pakistani soldiers contrasts with the relative silence about the deaths of "eight Afghan Local Police officers [who] were killed on Thursday morning by a [Taliban] roadside bomb that blew up as their truck passed by in the village of Pashtunabad in Logar Province."
That young Afghans pour into the streets when an Afghan soldier is killed by Pakistani soldiers, but do not react similarly when eight American-trained Afghan local policemen are killed by the Taliban, is worth noting. One could draw several possible conclusions. But the clashes between Afghan and Pakistani soldiers along the border may, to repeat, have little to do with the border itself, despite the NYT piece's mention of the Durand Line; in this sense it is different from the India-China border dispute. (I realize this is a debatable proposition, so reasoned disagreement is welcome.)