Why is that so often the pattern? I'd argue it's because there is yet another gap to close, and closing it might be one of the best things IT and CS can do together. The missing element is specification and documentation. The special apps programming team tends to be made up of bright people who are perhaps a little too impressed with what they think they already know, and an energetic can-do attitude, which is great for atmosphere but not so conducive to listening.
If that sounds familiar, it's because it's the story of special applications programming in industry since the dawn of time. And the industrial solution will work on campus, too: Every team needs a specs-and-docs member, who ideally is also on the testing/QA part of the team. (And if the team doesn't have that, we've just found another gap. They're everywhere!) If it's a student worker, you want someone who has at least had tech writing, but it will be better if they've had courses in specification writing or applications-oriented systems analysis. The faculty or grad student adviser may even want to work on some standardized reporting systems, which could make a nice senior or first-year-grad project in document systems design.
Clarifying communication, and making it accountable and testable, gives the student coding team a much more real-world-like work experience, and makes it far more likely they'll deliver something useful. The team wins, the users win and people go home happy.
And as a bonus, the spec-and-doc member is getting a great resume line, which just might help in closing that gap between successful student and employed professional.
I'll freely admit that on eight campuses, I've only seen special apps teams struggling and flailing, but there must be some out there that have succeeded. And I've never seen one that did anything other than send a proficient student programmer over to say, "So what do you need?"
Surely someone has a more positive experience to share. Why do you think they did better than what I'm describing? (Extra points awarded if they had a real spec-and-doc system in place!)