Ben;
I've been dealing with the same issue since last Tuesday (Tennessee Dept. of Education). On Tuesday afternoon, I published a new collection (Effective Practice Series), and it eventually showed up the following morning.
On Thursday afternoon, I added an additional track to this collection. Like your experience, it displays correctly in "Preview", but has yet to show up in the iTunes desktop application (Oddly enough, the new track DOES show up in the "Quick View" mode, but won't play. But when you open the Collection, the new track does not appear).
The new track DOES appear on both my iPad and iPhone, and I can preview the new track on both devices.
I contacted Apple iTunes U support, and they suggested that post on the discussion site, so that Apple's engineers who monitor the site could track the issue. I did receive a reply from one of Apple's engineers, but the problem persists (see related thread: "Site Manager Update Issue").
Hopefully, there will be an answer soon. All the best...
Syd Rodocker
Administrator, Tennessee Department of Education