UPDATE: My problems have been solved. See this post for details.
Myself an others are reporting about iPhone 2.0 Backup and Sync frustrations over on Apple’s discussion boards. The gist of the problem is iPhone 2.0 software attempts to do a full back up every time you sync. According to the Apple User’s Guide:
Once iPhone has been configured to sync with a particular computer, iTunes automatically makes a backup of iPhone on that computer when you sync. iTunes won’t automatically back up an iPhone that is not configured to sync with that computer. If you have configured iPhone to automatically sync with iTunes on a specific computer, iTunes will back up iPhone every time you connect it to that computer. Automatic syncing is turned on by default. iTunes only makes one backup each time you connect, even if you sync multiple times before disconnecting.
OK so there’s nothing really wrong with a backup right? There is when it takes 20-40 min each time. I’m sure this differs based on the amount of data you have on your phone. If you are in a hurry and in need of syncing some data sans a full backup, you can hit the “X” to skip the backup. iTunes should then proceed to sync your data and media.
If I find out any further details, I’ll post an update here. Feel free to add a comment below.