Communication fails when the participants in a conversation aren't talking about the same thing. This can be something as subtle as having slightly differing mappings of verbal space to conceptual space, or it can be a question of being on entirely different levels of conversation. There are at least four such levels: the level of facts, the level of status, the level of values, and the level of socialization. I suspect that many people with rationalist tendencies tend to operate primarily on the fact level and assume others to be doing so as well, which might lead to plenty of frustration.
The level of facts. This is the most straightforward one. When everyone is operating on the level of facts, they are detachedly trying to discover the truth about a certain subject. Pretty much nothing else than the facts matter.
The level of status. Probably the best way of explaining what happens when everyone is operating on the level of status is the following passage, originally found in Keith Johnstone's Impro:
MRS X: I had a nasty turn last week. I was standing in a queue waiting for my turn to go into the cinema when I felt ever so queer. Really, I thought I should faint or something.
[Mrs X is attempting to raise her status by having an interesting medical problem. Mrs Y immediately outdoes her.]MRS Y: You're lucky to have been going to a cinema. If I thought I could go to a cinema I should think I had nothing to complain of at all.
[Mrs Z now blocks Mrs Y.]
MRS Z: I know what Mrs X means. I feel just like that myself, only I should have had to leave the queue.
[Mrs Z is very talented in that she supports Mrs X against Mrs Y while at the same time claiming to be more worthy of interest, her condition more severe. Mr A now intervenes to lower them all by making their condition seem very ordinary.]
MR A: Have you tried stooping down? That makes the blood come back to your head. I expect you were feeling faint.
[Mrs X defends herself.]
MRS X: It's not really faint.
MRS Y: I always find it does a lot of good to try exercises. I don't know if that's what Mr A means.
[She seems to be joining forces with Mr A, but implies that he was unable to say what he meant. She doesn't say 'Is that what you mean?' but protects herself by her typically high-status circumlocution. Mrs Z now lowers everybody, and immediately lowers herself to avoid counterattack.]
MRS Z: I think you have to use your will-power. That's what worries me--I haven't got any.
[Mr B then intervenes, I suspect in a low-status way, or rather trying to be high-status but failing. It's impossible to be sure from just the words.]
MR B: I had something similar happen to me last week, only I wasn't standing in a queue. I was sitting at home quietly when...
[Mr C demolishes him.]
MR C: You were lucky to be sitting at home quietly. If I was able to do that I shouldn't think I had anything to grumble about. If you can't sit at home why don't you go to the cinema or something?
The level of values. Here the participants of a discussion are primarily attempting to signal their values. Any statements that on the surface refer to facts actually refer to values. For instance, "men and women are equally intelligent" might actually mean "men and women should be given equal treatment" while "there are differences in the intelligence of men and women" is taken to mean "it's justified to treat men and women unequally".
The level of socialization, also known as small talk. You aren't really talking about anything, but instead just enjoying the other's company. If the group is seeking to mainly operate on this level, someone trying to operate on the level of facts might get slapped down for perceived aggression if they insist on getting things factually correct.
For rationalists to succeed in spreading our ideas, we need to learn to recognize which level of conversation the discussion is operating on. One person acting on the level of facts and another on the level of values is a conversation that's certain to go nowhere. Also, it took me a while to realize that there have been occasions on which I was consciously trying to act on the level of facts, but my subconscious was operating on the level of status and got very defensive whenever my facts were challenged.
Usually what rationalists would want to do is to move the conversation to the level of facts. Unfortunately, if a person is operating on the level of values, they might perceive this as an underhanded attempt to undermine their values. I'm uncertain of what, exactly, would be the right approach in this kind of a situation. Defusing the level of status seems easier, as people will frequently find their unconscious jockeying for status silly once it's been brought to their conscious attention.
Nice to see you registered here. Do stick around. :)
A decent operationalization is rather tricky, especially since the levels mix and intertwine with each other, as others have pointed out. As for why the others look like fact-level exchanges... good question. Plausible deniability doesn't sound like a bad guess, especially in case of status games. Since a lot of the jockeying for status seems to happen without us even being consciously aware of it, there might also be a degree of self-deception involved. Though for what purpose, I am unsure.
Also, it might simply be the fact that it's easier to layer on new content on existing systems of communication than come up with entirely new ones. If most people are capable of keeping the different levels apart without conscious thought, then there's no particular reason to separate them more.
The definition of "rationalism" used on this site is somewhat different from the traditional rationalism vs. empiricism division - see this post. Of course, even going by our definition, it's not that an inability to differentiate between the levels would be part of the rationalist definition in any way (quite to the contrary). It's only that people drawn to the kind of analytical reasoning characteristic of rationalists tend to often have weaker social skills. (In other words, nerds are overrepresented among rationalists.)