Why are my iTunes backups getting slower?
Unfortunately iTunes doesn't handle the backup of third-party application data very well.
When it comes to your songs and movies iTunes is in charge of moving the data onto the device so it doesn't bother backing it up, it knows where it needs to put it again if the device is lost so it never moves it from the device back to iTunes. That's why you can have gigabyte upon gigabyte of songs and movies on your device and the backups are still fast. Those megabytes only go one way, into the device.
iTunes doesn't know about what apps from the app store need to keep though, so it moves all that data back onto your computer for safekeeping. If you ever lose your device it can make your new one just like the old one. It's great! but it takes time.
We've tried putting the comics in locations where iTunes won't back it up, but it just doesn't work.
The issue is that there are only two places where we can write data that doesn't get backed up. One of those places is erased every time the application starts, the other is erased whenever the device runs low on storage space or the application is updated.
Obviously neither one of those is suitable for storing your comics.
So what's the plan? Ourselves and many other developers have filed bug reports with Apple over this issue and it seems to be fixed in iOS4, so hopefully the fix will be with us in the next few weeks.
There is a great utility called BackOff available for free on Windows and Mac here:
There is a review of it at lifehacker here: http://lifehacker.com/5462514/
You can also stop a backup any time you like by pressing the little cross here: