The IF audience -- at least, the one we've got now -- is used to second-person narration. How distracting other people find it is hard for me to judge, because I've been used to this for *a long time now*, but I don't believe it's a major contributing factor in how most newcomers react to IF.
… it's everywhere! In a narrative, when we are told that “Gertrude got out of bed and made herself a cup of coffee for breakfast. In the afternoon she ate half a cucumber sandwich.”, we don't start wondering what happened to those hours between the coffee and the sandwich – of course we don't. But that's actually a convention, too, this excepting and understanding ellipses, though we usually don't pay attention to it. In real life, blacking out for the entire morning would be cause for alarm, but in a story it's a given if nothing interesting happens.
Many people accustomed to the so called realistic tradition in literature feel the first person narrator is pretentious, ranting and just way too artsy. (It's worth noting that the modern day realism in literature does actually enclose the “I”, too. But, back in the day, it didn't.) This, I think, happens in IF, too, just the other way around: anything that's not second person can be seen off-putting. That is, if you oppose all things artsy.
My own wording here reminds me:
I just wrote “if you
oppose” – an English language way to use the second person in a passive function. (In sentences such as: “In order to get in, you
need to buy a ticket.” It's possible that native English speakers don't see this a passive voice, but from an outsider point of view it functions as one.)
This “you-passive” caused debate here in Finland some years ago. Finnish doesn't (originally) have this grammatical device, but it made its way to our speech as a loan from English. As always in these kind of cases, this got people opposing “the wrong way of speaking”. The usual sarcastic response to someone using the “you” as a passive was to say something like “Well, it is not I
whose doing that.” It was almost like people were offended by this form of speech: like it was too presumptuous, trying to tell the other person what she was like.
However, I don't remember the last time someone complained about this. People have gotten used to it. The you-passive is still not an official form in the Finnish, and is frowned upon in literary style, but in spoken tongue it's pretty common. I remember when I played my first IF – it took some time to get used to the second person narrative. But not that long: by the end of that one single game I was used to it.
In the CYOA I'm working on I get around this by switching to a third person point of view and just straight up telling the player that while they get to influence the character's life, she's her own individual and not meant to represent the person reading the story.
I don't know what your CYOA is about, but if you word the disclaimer something like “character is her own individual and not meant to represent the person reading the story”, my first reaction is that this story must be something really gory or morally dubious – something requiring parental guidance (which is perfectly fine, of course, if it is that kind of story).