I keep having this problem; a few apps that download over and over and over...
I'm reasonably sure that the version I keep downloading via iTunes is actually the previous version, not the new update. For example the "Oz Weather" application is currently listed on the iTunes store as version 2.0, but the version I have in my library is 1.7.1. Another application, "Awesome Note (+Todo)", is version 2.0 in my library while the store suggests it has version 2.5 as the latest. When I check the "Mobile Applications" folder in my iTunes library, the files have the last modified date as the time I downloaded them (i.e. it does seem to be downloading them and putting them in the right place as far as I can tell), and the file sizes are approximately the same (within about 5-10 bytes) as the version I started with before the update process.
So I'm fairly sure this is either a problem with the app store; i.e. it's saying it has the new version but when the app is requested for download it's not actually the new version.
Or, it's a problem with iTunes (and the app store) where iTunes is requesting an older version for download (which I would think is pretty stupid if the app store actually supplies an older version). I'd be very surprised if this was the case.
The odd part though is that I dont' think this problem is happening for everyone... so my guess is that:
a) the app store is actually situated on a very large number of servers, or pushes files out using the Akamai service or similar.
b) one/some of the distributed servers is/are failing to keep up to date and are serving up out of date software
The fact that it seems to keep happening over and over to specific people might suggest that it's specific mirrors/akamai servers in specific locations (e.g. servers within particular ISPs, so all their customers will be getting data from that one server).
Of course a lot of the later part of this post is pure speculation, but hopefully this is of some use to the Apple support people who I'm really hoping actually read these threads.
Finally, I would suggest people try downloading applications in a few different places in case I'm right.
i.e. if you have a laptop with iTunes on it, try updating your apps at work, or at a friend's house, or a public wifi hot spot. Alternatively, just try downloading updates over the air if you have an iPhone (or again some other wifi location) to see if there's a reliable way to make the updates download properly. I found a little while ago that my updates all suddenly worked when I downloaded them over the air on my iPhone, but that might have just been coincidence...