I don't know where to go from there, because I never fixed it on my device. Reflashing, though, is not bad. I know how you feel, and I felt the same way when I first had to reflash my N900, but I assure you it's very painless. What's bad is restoring everything the way you had it, if you don't have backupmenu installed (and if you just unpack the backupmenu backups, you could easily bring in whatever file/code/setting was breaking the contacts-on-desktop shortcuts to begin with).

It's uninstallable but I don't think it would be easy and a reflash would be the only way I would do it - i.e. I know it's doable without reflashing but I wouldn't really undertake that effort myself.

And no, it's almost nothing to do with transitions (though if you count portrait-mode support as part of transitions then I suppose it's got a decent amount of transitions stuff); CSSU provides open source replacements for a few of the built-in packages, it provides for a bunch of advanced options in hildon-desktop (i.e., what Ctrl+Backspace does, whether or not Ctrl+Shift+Key or Ctrl+FN+Key send out dbus signals which you can then tie with dbus-scripts for other stuff, etc). There's a decent amount of minor bug fixes ported from upstream, including some major ones, like Qt apps not segfaulting when launched in portrait mode, and some minor ones like dark gray showing up correctly as a color in X-Terminal.

But if you didn't notice these things by now, you probably aren't affected by them much anyway. *Shrug*