I'm having this problem too. If I buy apps on my ipod and then sync it, iTunes will prompt me to copy them. It seems to start the process then gives up without any error message.
Also today I had my first app update (enigmo). I downloaded it in iTunes and sync'd my ipod. It flashed up "updating enigmo" then moved on to sync'd the rest of my content. On checking the app store still said engimo had an update. I then clicked sync in itunes and it started updating enigmo again but this time it took about 2-3mins.
riko