FWIW, I've found that downloading/upgrading ONLY direct via the iPhone (first generation) prevents such problems.
Last week, I bumped into the problems described here, always after itunes syncing -- where an upgraded app was included. Rebooting the iPhone usually worked. Monday, I was away from my desktop, so that's when I did the upgrade d/l to the phone. When I realized "hey, no hassles", I started using that method religiously. I've done this several times this week, and it's been smooth sailing.
(Of course, now that I've said that, the dang thing will probably futz up again. Fortunately, I use WinDoze, so such weirdness-on-the-eThing is anything but foreign to me. <sigh>)