Sex is complicated. But for Holden, and specifically for Holden's relationship with Jane, it's really complicated. We talk in Holden's "Character Analysis" about how he can't imagine getting too sexy with a girl he has genuine emotion for, and Jane is a prime example. They hold hands, they sit close to each other, Jane puts her hand on the back of his neck…cute, but not exactly the most exciting Friday night with your significant other. Again, this was the 1940s, but as we see from the other boys at Pencey, young relationships aren't devoid of fooling around. We can't blame Holden's lack of advances on old-fashioned values – we have to look further.
The most telling scene is one we get in a flashback. The checker-playing scene is to Jane's character what the baseball mitt is to Allie's. We lead into it sort of accidentally (Holden just sits down in a "vomity-looking" chair in the hotel lobby and ruminates), and he delivers the crucial information we've been looking for.
Well, he sort of delivers it. Much like the Mr. Antolini incident, Holden leaves it up in the air as to whether or not Jane has been the victim of sexual abuse at the hands of her stepfather. Holden's not sure, so we're not sure (although we can take a pretty good guess). Even if Jane's step-father hasn't raped, we know there's at least something wrong; Jane refuses to look the man in the face and cries after he leaves the room. Either way, it's not a good relationship, and Holden's suspicions that sexuality have something to do with it don't seem far off the mark (especially considering his earlier statement, back in Chapter Four, that her "booze-hound" stepfather used to run around the house naked).
So this, combined with Holden's history of possible sexual abuse, is a pretty good reason for their stunted sexual relationship. What's great is that it doesn't inhibit their emotional relationship at all – look at how Holden describes Jane to Stradlater. She keeps her kings in the back row, she used to be a dancer, she was a terrible golfer. Holden remembers personal, revealing details. He doesn't focus on the physical, as someone like Stradlater might, and he obviously cares about Jane as a person.
Of course, Holden's inability to reach out to Jane despite his feelings is a big reminder of his passivity and indecision. When he finds out she's downstairs waiting for Stradlater, he says over and over that he'll go down to say hello, but never does. He repeatedly contemplates calling her once he's in New York, but can't bring himself to go through with it. When he finally does pick up the phone already, she's not there.