Since the release of the App Store for the iPhone and iPod touch last week, I’ve been busy filling my iPhone (and emptying my pocketbook) with any number of fun, useful, or just plain interesting applications. As of now, my iPhone is home to no less than 40 third-party applications, and I expect that number to continue growing. Much as the iTunes Music Store changed the music business when it launched in April of 2003, I believe the App Store has changed the mobile software distribution business…but that’s a discussion for another day.

In order to use the App Store, I had to upgrade my iPhone to the new 2.0 software release, a process I wasn’t exactly looking forward to. However, after taking the leap, I’m very happy with the quality of App Store programs to date. After only a few days, I’m only missing a couple key programs from my iPhone’s prior collection, and I would expect those programs to appear in the App Store soon. Beyond the App Store, there’s more good stuff to be found in the 2.0 version of the iPhone’s software.

In the midst of all this glorious good news, however, there’s this one annoying new feature in iPhone 2.0 software…and it’s such an annoying feature that my hand trembles whenever it approaches my Mac Pro’s iPhone docking station, to drop the iPhone in for a routine sync. Well, OK, maybe my hand doesn’t really tremble, but I do approach this routine task with a great amount of trepidation, delaying it as long as possible. What feature could actually be so bad that I feared seeing it in action, you might ask?

This is the cause of my syncing angst—that little progress bar—which is part of a fun game I like to call the “iPhone Backup Lottery,” or IBL for short. How do you play the IBL? It’s simple—just plug in your iPhone (or iPod touch, I imagine), and then wait. If you’ve won the IBL, the backing-up progress bar will rapidly fill from left to right, followed by the start of the usual iPhone syncing process.

If, as is usually the case with lotteries, you’ve lost the IBL, then the progress bar moves more slowly than does the release cycle for major versions of Microsoft Windows. In my case, my current personal record as an IBL loser is 74 minutes from the time I docked the iPhone until the backup completed. As it turns out, though, I’m far from a record-setter. My Macworld colleague Dan Frakes reports that he’s had a backup take more than two hours!

On those oh-so-rare occasions when I’ve won the IBL, it’s taken as “little” as three or four minutes for the backup to complete. Once the backup completes, the actual sync takes but a couple of minutes.

I found this new behavior so annoying, I was positive it had to be a bug—I even went so far as to restore my iPhone to factory stock and upgrade it again, just to be sure (no luck; I was still an unwilling participant in the IBL). Just as I finished doing that, though, I found that this isn’t a bug, it’s a feature:

If you have configured your iPhone or iPod touch to automatically sync with iTunes on a specific computer, iTunes will back up the iPhone or iPod touch after you connect it to that computer and sync with iTunes. … iTunes only makes one backup each time you connect, even if you sync multiple times before disconnecting.

That’s right, these constant backups are a feature, not a bug. It’s an intentional behavior, but apparently only for those of us who automatically sync. Believing that I’d found a way out of the IBL, I switched my iPhone’s preferences to manual sync—a press of the Sync button was a small price to pay for not playing the IBL. At first, it seemed to work fine—I connected my phone, clicked the Sync button, then watched it do just that. Success! But no…the IBL was merely teasing me, as a backup started immediately after the sync completed. As usual, I lost the IBL, and freed my iPhone from its cradle roughly an hour later.

So really…what’s going on here? I understand that there may be programs I installed directly on the iPhone from the App Store, and those need to be backed up. Similarly, I may have changed data within an application, and that also needs to be backed up. But there’s seemingly no rhyme or reason to the backup madness. I can connect my phone, let it run a full backup and sync, disconnect it, let it sit on the desk for three minutes, then connect it again…and get hit with another hour-long backup cycle. On other occasions, though, it seems I can take my iPhone away, do some work with it, drop it in the cradle, and have “only” a 10-minute backup cycle. If there’s a rationale for the length of the backup cycle, I haven’t figured it out yet.

In talking with other iPhone users, it seems all are seeing this backup process, but for some users, the time required isn’t bad at all. Based on conversations with these users, it appears the duration of the backup is related to the number of installed programs—the more you have, the longer the backup takes. While this makes logical sense, it doesn’t explain why sometimes the process only takes a few minutes instead of an hour-plus for my 40-application iPhone.

Even with 40 applications, though, a backup shouldn’t take anywhere near an hour—there’s just not that much data in there to push around. I know Apple wants to help keep my data safe, and I laud the company for that. However, the current implementation of backup in iPhone 2.0 seems very broken to me.

Because the process is so tediously slow, I’ve implemented a solution that lets me sync my iPhone more than a couple times a day—I simply press the “x” (cancel) button in the iTunes info window to cancel the backup. Yes, this means I don’t have a local backup, and I’ll have to reload all my movies, songs, contacts and whatnot should I experience an iPhone disaster. (App Store programs are tracked separately, and can be downloaded again if necessary, for free. Any data I stored with those programs, however, would be lost.) Even if it comes this, though, that would be a one-time process that doesn’t take all that much time—especially when compared to a one-hour delay every time I sync my iPhone.

Those backup files, though, may not be of much help in case of an iPhone restore. Thanks to some instability in the apps and iPhone 2.0 software, Dan Frakes has had to restore his iPhone 3G a few times already. After waiting through many lengthy backup cycles, he figured he’d at least be able to use a backup to get his phone back to its as-configured state. Alas, that was not to be the case, as he’s seen this dialog box every time he’s had to restore:

Given Dan’s lack of success with restoring from backup, I’m willing to live with the risk of running backup-free. However, I’m hoping that this backup process is patched in a future iPhone and/or Mac software update, so that I can once again have complete local backups—ones that don’t take hours to create, and work when needed.