Hi all,
So I am having this issue too, and it's extremely annoying. Like the OP, I bought the Mac Box Set for Snow Leopard, which came with iLife and iWork '09.
I tried all the regular stuff...deleting the apps and all preferences associated with iWork, reinstalling from the original disc, and then applying the update again. First tried the update the Mac App Store gives me, and then found and downloaded the standalone updater on Apple's support site--which, I should mention, Apple recommends if you installed iWork from a physical disc.
So I just wanted to let everyone know, I contacted Apple Support about this issue (via the Mac App Store support email form), explained my issue, and asked for download codes for all the MAS versions of the iWork apps. I believe this would fix the issue, as everyone having the problem seems to have originally gotten iWork as a boxed copy. I'll update when Apple responds--I believe I should be entitled to free downloads for the MAS versions of iWork if they can't get it to work. I'll keep you guys posted!
Adam
P.S. Haven't tried repairing permissions, will try that now just in case, although I can't remember a time in the last 5 years or so when that fixed any problem I've ever had.
Update: Just tried repairing permissions, it did nothing. Another thing I should mention: before Mountain Lion, I hadn't attempted to use any iWork app in a long time, as I wasn't in school currently and didn't really have a reason to use it over the simple TextEdit. So the version I had was probably quite old, and was never updated after the Mac App Store was released, which I assume is the reason I'm having the update issues. And when I install them straight from the disc before attempting the 9.2 updater, the app just quits immediately giving an error that it can't be opened and to reinstall.