I can think of a few books with romantic plotlines where something other than a misunderstanding played a major role. Shards of Honor, for instance, featured a star-spanning culture clash erupting into warfare. Some other possible conflicts:
* The characters were raised so differently that it creates many differences in how they do everyday things, so that they have a hard time fitting together.
* The characters hold deeply opposed religious/political/other views that spark interpersonal disputes and make their relatives uncomfortable, and which cannot easily be abandoned.
* The characters live far apart. It is difficult for them to spend time together, even though they both want to.
* The characters live in a context where extreme social disapproval makes it difficult or even dangerous for them to be together, which will continue as long as they are in a relationship. Or even alive, for some cases.
* The characters don't have a language in common. One or both will have to learn a new language, which for most people is exhaustive and frustrating.
* There is an inherent physical risk to them being together, especially in a sexual way. This is most prevalent in speculative fiction with a vampiric or lycanthropic or alien partner but there are other possibilities.
* The characters have opposing professions, which they are unwilling or unable to change.
* One character wants children and the other does not (or cannot have them). No matter how much they love each other, they want fundamentally different things from life in that regard.
* One character is handicapped. The other is not used to working around that and feels uncomfortable.
Once in a while, I see one of those other factors played as the prevailing conflict that the characters must come to terms with before affirming their relationship. Most of the time, though, even when these very big issues are on the board -- these things that frequently lead to breakups -- they are usually overshadowed by Misunderstanding #1, as if love solves everything. It doesn't. It really, really doesn't. It can make you determined to solve everything, but that's a different story.
That's a different story, and that's the kind I want to read, and write myself.
One of the other things that got me thinking about this was the planned relationship between Fala and Rai in Torn World. She's Northern, he's Southern; relationships are strained between those cultures, but they can't easily ignore each other anymore. Their everyday lives are so different as to have almost no overlap. Social support for the relationship is variable; some of their relatives are okay with it, but the expectations are so wildly different that even "support" can spark outbursts. Their homes are very far apart; they have to figure out where or when they could be together and whether they can stand to separate sometimes. At the time they meet, they are both handicapped: Rai was born blind, and Fala lost her legs in a wilderness accident. It doesn't help that he's relatively comfortable with his handicap and she isn't with hers yet. Their languages share a common root (Ancient) but have evolved differently for Fala (Northern) and Rai (Southern). The grammar and function words are similar, but a lot of the content words are very different. That puts a drag on the conversation. They're lucky that both of them are smart, fast learners -- and Rai has a stupendous memory.
Do they love each other? Once they get over some initial awkwardness, yes, they both understand that part just fine. It doesn't help much with problem-solving. It just keeps them in a place where they need to solve those problems. Sort of like the difference between holding someone over a fire vs. giving them a fire extinguisher.