Just wanted to take a run at this one right quick. I don't know what this player's specific issue is but there seems to be an undercurrent of dissatisfaction from players who are always looking at their deployable resources before considering the fiction (rather than the inverse). So many people are driven by tangible, visual elements before them that their creative juices are stunted when lacking such cues. Even for creative players (who are fiction first and have a deeply creative reservoir), visual cues can help. To that end, I have a prop technique for you that I use at my home table.
It is basically stolen from Fate Aspects and MHRP scene Distinctions. I keep flashcards to scrawl information on when I'm running a game. When I'm running a Skill Challenge, I will write a two/three word phrase that represents the thematic, evocative elements of the scene when I frame it ("Cold, Dark Night", "Buzzing Marketplace", "Simmering Rage", "Craggy, Dead Tundra", "Playing Children", etc). This gives players visual cues to consider first (fiction-first) to riff off of when considering the environment, the situation, and their response. As the challenge evolves, I'll add more and take some away (as fitting) until it revolves itself.
If that is this player's problem, this should help.
I'm not sure what his problem is. He doesn't seem to have a problem engaging with stuff during the skill challenge, as he comes up with uses for his skills very easily (Religion checks to ask his goddess in help closing the Portal, Arcana checks to scan for magical traces that he can note / track, Heal checks to keep the party healthy / looking good / make sure they're not leaving a blood trail, Perception checks to keep an eye out for particular dangers tied to whatever is going on, etc.).
Whatever his problem is, it's fairly deep, though. He's said that "skill challenges are the part of 4e I hate most", and while it seems like he's more than willing to tolerate them to keep playing (he really likes the game / campaign), he doesn't seem to enjoy them afterwards. Sometimes I can see the him get lost in the really tense skill challenges, but he did make a comment in the middle of the cave-in escape skill challenge that he hated skill challenges, though it was just after he got dropped from some falling rocks. And, as I've noted before, he first brought up his issue with them after the investigation skill challenge, in which they rolled low a lot and nearly failed.
I think that it's possible that he simply doesn't like losing, or getting close to it. I've seen him tense up during the harder combats, but that's normal enough. If this is the problem, I know there's nothing I can do to resolve it; I'm not about to make things consistently easy. That's not fun for me, as I really like it when tension pops up, and then the players (hopefully) overcome the obstacle. I also don't mind them dominating at times, though. I like both, not just one.
I'll have to try to get a better feel for it. I don't think his problem is an inability to engage with the context of the current challenge. I've only got observations to go on, as he couldn't come up with an answer when I asked what he disliked about it. Maybe if I approach him again and tell him I want to know what it is so that I can see if I can work with it, that'll make it easier for him to share. For all I know, it's simply the forced narrative structure (not that he would use a phrase like that). If that's the case, there's no way for me to change skill challenges enough to really help his tastes that I can think of, as that would seemingly work directly against the point of skill challenges. I'll talk to him again and get back to you guys.